In the present work, isoenzyme electrophoresis was used to analyze the variability and phenetic relationships among seven American species of genus Prosopis belonging to three different sections: P. argentina (Monilicarpa), P. glandulosa, P. velutina, P. flexuosa, P. ruscifolia, P. kuntzei (Algarobia), and P. reptans (Strombocarpa). The genetic variability in P. argentina, P. reptans, and P. kuntzei was significantly lower than in the rest of the species analyzed. The species belonging to different sections are highly differentiated, but the relationships retrieved among species belonging to the section Algarobia suggested that the series of this section are not natural groups. P. kuntzei is as differentiated from the remaining species of Algarobia as from P. reptans or P. argentina, suggesting that this species might be included in a different section. The series within section Algarobia are not supported by the clusters retrieved in the phenogram based on isoenzymatic data. The results suggest that the two North American species (P. velutina and P. glandulosa) would have originated in different founder events.