In this study, the variation of morphological and agronomic characters of 10 accessions of J. curcas selected from Yucatan, Mexico, and Honduras was analyzed. The characters associated with the proportions of the plants (height, number, and length of branches), the fruits (diameter and thickness), and the seeds (length, width, and volume), as well as those associated with the agronomic yield (number and yield of seeds plant− 1), explained the greatest variation between the accessions, 40 and 24%, respectively. The CAM32 and GAGI10 accessions had the lowest vegetative proportions and the highest agronomic yield, SUCILATEBEC and B5F59P19 had the lowest proportion and low yield, B3F119P1 had the highest proportion and high oil content, but low yield; while B5F83P1 had high values of vegetative proportions, and agronomic performance. The characters with the greatest variation among the accessions were ABM (59.93%), WV (56.91%), NS plant− 1 (57.18%), the SY plant− 1 (55.49%), and NL (54.37%). The similarity analysis grouped the accessions that had in common the geographical origin and the magnitudes of the characters associated with the agronomic performance and with the proportions of the plants, fruits, and seeds. The present study allowed the identification of J. curcas accessions with desirable agronomic and morphological traits, such as seed yield, oil content, and plant height, which can serve as progenitors in breeding programs for this species.