Kreuzer, M., Tribsch, A. & Nyffeler, R. 2014. Ecological and genetic differentiation of two subspecies of Saussurea alpina in the Western Alps. Alpine Botany 124: 49-58.
Baltisberger, M., Nyffeler, R.. & Widmer, A. 2013. Systematische Botanik: einheimische Farn- und Samenpflanzen. Zürich, vdf Hochschulverlag.
Figueiredo, E., Smith, G. F. & Nyffeler, R. 2013. August Wulfhorst (1861-1936) and his overlooked contributions on the flora of Angola. Candollea 68: 123-131.
Nyffeler, R. 2013. Neuerungen in der Klassifikation der einheimischen Gefässpflanzen. infoflora 2: 40-46.
Nyffeler, R. 2012. Einblicke in die botanische Sammeltätigkeit von Hans Schinz während seiner Reise durch Südwestafrika. In: Beckmann, G. et al. (eds.); "Man muss eben Alles sammeln": der Zürcher Botaniker und Forschungsreisende Hans Schinz und seine ethnographische Sammlung Südwestafrika, pp. 119-126. Zürich, NZZ Libro.
Steudel, B., Kessler, M. & Nyffeler, R. 2012. Using the internet to aid in discovery of unrecognized type material. Phytotaxa 62: 13-24.
Wohlgemuth, T., Bachmann, P., Bergamini, A., Burnand, J., Ginzler, Ch., Keel, A., Kessler, M., Nobis, M., Nyffeler, R., Röthlisberger, J., Spillmann, J., Wyss, G. 2012. 173 Jahre nach Kölliker: Zeit für eine neue Flora des Kantons Zürich. Vierteljahrsschrift der Naturforschenden Gesellschaft in Zürich 157(1/2): 9-22.
Arakaki, M., Christin, P. A., Nyffeler, R., Lendel, A., Eggli, U., Ogburn, R. M., Spriggs, E., Moore, M. J. & Edwards, E. J. 2011. Contemporaneous and recent radiations of the world's major succulent plant lineages. Proceedings of the National Academy of Sciences 108: 8379-8384.
Nyffeler, R. & Eggli, U. 2010. A farewell to dated ideas and concepts - molecular phylogenetics and a revised suprageneric classification of the family Cactaceae. Schumannia 6: 109-149.
Nyffeler, R. & Eggli, U. 2010. An up-to-date familial and suprafamilial classification of succulent plants. Bradleya 28: 125-144. [as pdf]
Linder, H. P., Johnson, S. D., Kuhlmann, M., Matthee, C. A., Nyffeler, R. & Swartz, E. R. 2010. Biotic diversity in the Southern African winter-rainfall region. Current Opinion in Environmental Sustainability 2: 1-8.
Nyffeler, R. & Eggli, U. 2010. Disintegrating Portulacaceae - a new familial classification of the suborder Portulacineae (Caryophyllales) based on molecular and morphological investigations. Taxon 59: 227-240. [online access (if available)]
Eggli, U. & Nyffeler, R. 2009. Living under temporarily arid conditions - succulence as an adaptive strategy. Bradley 27: 13-36, ills. [as pdf]
Eggli, U., Marchesi, E., Bonifacino, M. & Nyffeler, R. 2008. Taxonomy and distribution of epiphytic cacti in Uruguay. Notes towards a checklist of Cactaceae of Uruguay, 3. Haseltonia 14: 161-169, ills, maps. [as pdf]
Nyffeler, R., Eggli, U., Ogburn, M. & Edwards, E. 2008. Variations on a theme: repeated evolution of succulent life forms in the Portulacineae (Caryophyllales). Haseltonia 14: 26-36. [as pdf]
Eggli, U., Machado, M. & Nyffeler, R. 2008. Nomenclatural note on the subgenera of Parodia (Cactaceae - Cactoideae). Taxon 57(3): 985-988.
Machado, M. C., Nyffeler, R., Eggli, U. & Larocca e Silva, J. F. 2008. A new species of Parodia (Cactaceae, Notocacteae) from Rio Grande do Sul, Brazil. Novon 18: 214-219. [as pdf]
Eggli, U. & Nyffeler, R. 2007. Parodia allosiphon (Marchesi) N. P. Taylor (Cactaceae - Cactoideae) - a cladistically 'basal' species with a restricted distribution range. (Notes towards a checklist of Cactaceae of Uruguay, 2). Bradleya 25: 37-44. [as pdf]
Nyffeler, R. 2007. The closest relatives of cacti: insights from phylogenetic analyses of chloroplast and mitochondrial sequences - with special emphasis on relationships in the tribe Anacampseroteae. American Journal of Botany 94: 89 - 101.
Muñoz, F., Eggli, U. & Nyffeler, R. 2006. Opuntias en Maldonado, Uruguay. Quepo 20: 84 - 90.
Edwards, E., Nyffeler, R. & Donoghue, M. J. 2005. Basal cactus phylogeny: implications of Pereskia paraphyly for the transition to the cactus life form. American Journal of Botany 92: 1177-1188.
Nyffeler, R., Bayer, C., Alverson, W. S., Yen, A., Whitlock, B. A., Chase, M. W. & Baum, D. A. 2005. Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences. Organisms, Diversity & Evolution 5: 109-125.
Ackerly, D. A. & Nyffeler, R. 2004. Evolutionary diversification of continuous traits: phylogenetic tests and application to seed size in the California flora. Evol. Ecol. 18: 249-272.
Baum, D. A., DeWitt Smith, S., Yen, A., Alverson, W. S., Nyffeler, R., Whitlock, B. A. & Oldham, R. L. 2004. Phylogenetic relationships of Malvatheca (Bombacoideae and Malvoideae; Malvaceae sensu lato) as inferred from plastid DNA sequences. Amer. J. Bot. 91: 1863-1871.
Mast, A. R. & Nyffeler, R. 2003. Using a null model to recognize significant co-occurrence prior to identifying candidate areas of endemism. Syst. Biol. 52: 271-280.
Nyffeler, R. 2003. Aeonium (Crassulaceae). In: Eggli, U. (ed.); Illustrated Handbook of Succulent Plants: Crassulaceae. Pp. 15-23. Heidelberg: Springer-Verlag.
Nyffeler, R. 2003. Aichryson (Crassulaceae). In: Eggli, U. (ed.); Illustrated Handbook of Succulent Plants: Crassulaceae. Pp. 24-27. Heidelberg: Springer-Verlag.
Nyffeler, R. 2003. Monanthes (Crassulaceae). In: Eggli, U. (ed.); Illustrated Handbook of Succulent Plants: Crassulaceae. Pp. 183-186. Heidelberg: Springer-Verlag.
Nyffeler, R. & Rowley, G. D. 2002. Piperaceae. In: Eggli, U. (ed.); Illustrated Handbook of Succulent Plants: Dicotyledonous Families. Pp. 362-369. Heidelberg: Springer-Verlag
Nyffeler, R. 2002. Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/matK and trnL-trnF sequences. American Journal of Botany 89: 312-326.
Nyffeler, R. & Baum, D. A. 2001. Systematics and character evolution in Durio (/Malvaceae/Helicteroideae/Durioneae or Bombacaceae-Durioneae). Organisms Diversity & Evolution 1: 165-178.
Nyffeler, R. 2001. What about the tribe Notocacteae? Cactus Systematics Initiative 12: 25-27.
Nyffeler, R. & Baum, D. A. 2000. Phylogenetic relationships of the durians (Bombacaceae-Durioneae or /Malvaceae/Helicteroideae/Durioneae) based on chloroplast and nuclear ribosomal DNA sequences. Plant Systematics and Evolution 224: 55-82.
Nyffeler, R. & Eggli, U. 2000. Similarity is only skin-deep: the use of comparative plant anatomy as illustrated by a study of columnar cacti from Chile (Eulychnia and Echinopsis, Cactaceae). Botanica Helvetica 110: 1-10.
Nyffeler, R. 2000. Should Pfeiffera be resurrected? Cactus Systematics Initiative 10: 17-18.
Alverson, W. S., Whitlock, B. A., Nyffeler, R., Bayer, C. & Baum, D. A. 1999. Phylogeny of the core Malvales: evidence from ndhF sequence data. American Journal of Botany 86: 1476-1486.
Nyffeler, R. 1999. A new ordinal classification of flowering plants. Trends in Ecology and Evolution 14: 168-170.
Nyffeler, R. 1999. Notocactus versus Parodia - the search for a generic classification of the subtribe Notocactinae. Cactus Consensus Initiatives 7: 6-8.
Baum, D. A., Alverson. W. S. & Nyffeler, R. 1998. A durian by any other name: taxonomy and nomenclature of the core Malvales. Harvard Papers in Botany 3: 315-330.
Nyffeler, R. 1998. The genus Uebelmannia (Cactaceae). Botanische Jahrbücher für Pflanzensystematik 120: 145-163.
Eggli, U. & Nyffeler, R. 1998. Proposal to conserve Parodia against Frailea. Taxon 47: 475-476.
Nyffeler, R., Eggli, U. & Leuenberger, B. E. 1997. Noteworthy idioblastic sclereids in the stems of Eulychnia (Cactaceae). American Journal of Botany 84: 1192-1197.
Nyffeler, R. 1997. Stem anatomy of Uebelmannia (Cactaceae) - with special reference to Uebelmannia gummifera. Botanica Acta 110: 489-495.
Nyffeler, R. & Eggli, U. 1997. Comparative stem anatomy and systematics of Eriosyce s.l. (Cactaceae). Annals of Botany 80: 767-786.
Nyffeler, R. 1997. Notes on the taxonomy of Austrocactus. Cactus Consensus Initiatives 4: 14.
Nyffeler, R. & Eggli, U. 1996. Berger's 'Kakteen' - The end of a nomenclatural nightmare in sight? Taxon 45: 301-304.
Nyffeler, R. & Plestil, V. 1996. Sedum surculosum Coss. Sedum Society Newsletter 38: 12-13, 15-16.
Nyffeler, R. 1995. Hybridization in Monanthes. In: 't Hart, H. & Eggli, U. (eds.); Evolution and Systematics of the Crassulaceae; pp. 76 - 88, ills. Leiden: Backhuys Publishers.
Eggli, U., 't Hart, H. & Nyffeler, R. 1995. Towards a consensus classification of the Crassulaceae. In: 't Hart, H. & Eggli, U. (eds.); Evolution and Systematics of the Crassulaceae; pp. 173 - 192. Leiden: Backhuys Publishers.
Nyffeler, R. 1995. Die Gattung Monanthes Haworth. Kakteen und andere Sukkulenten 46: 157 - 165.
Nyffeler, R. 1995. Nomenklatorisches zur Frage 'Echinofossulocactus oder Stenocactus'. Kakteen und andere Sukkulenten 46: 265 - 268.
Nyffeler, R. 1995. Die Gattung Monanthes Haworth. Kakteen und andere Sukkulenten 46: 157 - 165.
Nyffeler, R. & Eggli, U. 1994. Die Konsensusklassifikation der Kakteen. Kakteen und andere Sukkulenten 45: 142 - 149.
Nyffeler, R. 1992. Zur korrekten Schreibweise von nach Jos Arechavaleta y Balpardo benannten Arten. Internoto 13: 113.
Nyffeler, R. 1992. A taxonomic revision of the genus Monanthes Haworth (Crassulaceae). Bradleya 10: 49 - 82.
Nyffeler, R. 1991. Beitrag zum Problem der Sprossungsformen bei Notokakteen. Internoto 12: 132 - 135.