The taxonomic status of a specimen of the genus Jaltomata recovered from the Central Highland Valley of Mexico was realized. Phylogenetic analysis was performed via Bayesian inference and maximum likelihood methods complemented with Genealogical Concordance Phylogenetic Species Recognition (GCPSR) using the PHI test. The results indicated that the specimen in study belongs to the genus Jaltomata sp. nov. supported by PHI test (φ=1.0) showing no evidence of recombination. Characteristics of corolla, pedicel and calyx, stigma, anthers, fruit, and seeds, differentiated this species. Based on the results, the name Jaltomata tlaxcala is proposed for this new species.