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. Zapoteca subgenus Ravenia is included in Z. subgenus Zapoteca, Z. quichoi is transferred from Z. subgenus Amazonica to Z. subgenus Zapoteca, Z. sousae is included in Z. subgenus Zapoteca, and the new subgenus Zapoteca subgenus Subamazonica is described to accommodate the species Z. filipes and Z. scutellifera. A key to the subgenera is presented.