At present, little is known about Opuntia seed proteins and their contribution to the characterization and taxonomy of genotypes belong to this genus. The variation among 102 accessions of Mexican Opuntia was studied using electrophoretic patterns by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of their seed total proteins (STPs) and seed storage proteins (SSPs). Albumins and globulins were the most abundant protein fractions, with contents varied from 2.6 to 11.9mg/mL and 2.6-9.5mg/mL, respectively. These were followed by glutelins (2.3-8.5mg/mL) and prolamins as the lowest (1.1-7.9mg/mL) of the four protein factions. On the other hand, STPs content varied between 1.13 and 7.12mg/mL. Regardless of variations in protein content estimated in seeds, the electrophoretic patterns of STPs and SSPs, as outcome of their SDS-PAGE, were not so variable. Furthermore, the individual analysis of each STPs or the SSPs analyses, separately, were not enough to discriminate all accessions, since it was necessary to combine the data resulting from all protein profiles together to differentiate all Opuntia genotypes. The UPGMA analysis indicated that there is no separation between accessions of species of the prickly pear (sweet fruits) and ". xoconostle" (acidic fruits), even though the latter were grouped together. Based on biochemical markers analyzed herein, the need for revision of taxonomic assignment of genotypes belonging to the genus Opuntia is suggested.