This article contains metadata related to the research article "Behavior of genetic diversity in F1 crosses of selected accessions of Jatropha curcas" (Sánchez-Velázquez et al., 2018). The data presented in this article belong to a diversity study using ISSR molecular markers of a J. curcas germplasm collection that includes bred offspring and analysis of similarity between accessions. We tested previously reported primers in PCR assays to obtain a genetic profile of the accessions. These profiles were used to calculate Dice similarities. Similarity between offspring and parentals can be compared either with the maternal side or paternal side.