We tested the species hypotheses for 8 of the 9 Phloeosinus spp. inhabiting the Transition Zone of Mexico based on molecular and morphological data. The morphology was analyzed using various trait sources, considering the geographical variation for each taxon by mean multivariate analyses. Through genomic analyses using genotyping by sequencing paired-end data, including genetic structure, phylogenomic, and species delimitation analyses, we evaluate whether the taxonomic species correspond to well-structured lineages that are congruent with their morphological variation and taxonomic classification. Our results supported Phloeosinus baumanni, P. deleoni, P. serratus, and P. tacubayae as genetically differentiated and well-structured lineages. These species in addition to P. arizonicus, P. cristatus, P. spinosus, and P. taxodii tacodiicolens display discrete phenotypes, either in one or several components of their morphology and considering their geographical variation, thus agreeing with their taxonomic hypothesis. Phloeosinus serratus represents a special case of all the taxa analyzed. This species showed high morphological polymorphism associated with specimens from 3 host species and different localities. However, these correspond to a single panmictic genetic population, with varying degrees of intermixture, without phylogenetic lineages structured by the host. Thus, it corresponds to only one species with wide phenotypic plasticity likely associated with patchy areas of different host species. Phylogenomic topologies support at least 2 diversification hypotheses for Phloeosinus spp. in the MexicanTransition Zone; one of them implies the specialization of feeding preferences toward Cupressus, from Juniperus habits, and the other one the presence of 2 big clades specialized in Cupressus, and Juniperus spp., respectively.