The electrophoretic patterns of α- and β-isozyme esterases from seeds of 44 populations belonging to twelve Petrocoptis taxa were compared in order to clarify taxonomic relationships within the genus. Electrophoretic zymograms showed the presence of 20 electromorphs, which yield 24 α-esterase and 22 β-esterase phenotypes. Most of the bands and the electrophoretic profiles were restricted to a few localities and taxa. Correlation between isozyme similarity and geographic distance among populations was not detected, as revealed by the Mantel test (r = 0.007; p = 0.5811), suggesting that there was no greater phenetic similarity among neighboring populations than among distant populations. Multivariate analysis of the data (Factorial Correspondence Analysis and Multidimensional Scaling) did not depict a consistent picture of the taxonomic relationships within the genus, probably due to the high intraspecific variability present in some taxa. Given this polymorphism within some Petrocoptis taxa, esterase isozymes do not provide exclusive markers for the different species. However, the data partly support the splitting of the genus into two broad allopatric groups.