The subgeneric classification of the neotropical legume genus Zapoteca is revised based on an analysis of the nuclear ETS and ITS, and the plastid trnL-trnF DNA-regions. Subgenus Ravenia is included in subg. Zapoteca, Z. quichoi is transferred from subg. Amazonica to subg. Zapoteca, Z. sousae is included in subg. Zapoteca and one new subgenus, subg. Subamazonica, is described to accommodate the species Z. filipes and Z. scutellifera. A key to the subgenera is presented.

Multiple DNA-sequence alignments of ETS, ITS and trnL-trnF of the neotropical genus Zapoteca (Fabaceae) and tree files resulting from Bayesian inference analyses.