Faba bean crop (Vicia faba L.) is important in México, it is a legume rich in protein and its market price is higher than those of maize and bean; however, in recent years there has been a significant decline in its performance. The aim of this study was to determine the genetic variability and analyze the relationship between 39 faba bean accessions using inter simple sequence repeats (ISSR) markers. Accessions of faba bean were collected according to their best phenotypic characteristics, later they were molecularly characterized. With the obtained band registration, a binary data matrix was built to perform the corresponding statistical analysis. The utilized ISSR markers produced 142 fixed and repeatable bands, of which 134 were polymorphic. The values of resolution power (Rp), polymorphic information content (PIC), and marker index (MI), respectively indicated that primer 848 was the most efficient to analyze genetic variability with values of 12.8, 0.40, and 8.06, respectively, followed by primers 857 and ISSR2M. Genetic distances oscillated between 0.38 and 0.83, and verified the groupings observed in the dendrogram, which indicates high variability at the level of DNA among the analyzed genotypes, observing six defined groups according to UPGMA analysis. In the analysis of main components the registered groupings were determined by the origin of the gathering. The use of ISSR markers was efficient to characterize at the level of DNA the assessed bean accessions, indicating the existence of variability, the identified contrasting accessions can be utilized in genetic improvement programs aimed at solving the needs of the producers.