It is important to include in breeding programs the selection by the relationship of kinship by molecular markers. Based on the above, the objective of this study was to establish relations of kinship between hybrids F1 of cocoa of crosses ICS 195 x INIFAP 1 and INIFAP 1 × ICS 95. The markers used were based on microsatellite (SSR): mTcIR mTcCIR 8 and mTcCIR 24 as well as inter simple sequence repeats (ISSR): 829 UBC, UBC 835 and UBC 841. The results showed 100% of polymorphic alleles between maternal and paternal parent. These markers allowed to identify 58 hybrids F1 of a total of 61. According to the markers used and their corresponding values of polymorphic information content (PIC), these were informative, which guarantees that the markers used in this investigation are reliable and they allow to identify hybrids based on their kinship.