Species delimitation within Polyphagotarsonemus latus sensu lato was evaluated using an integrative taxonomy approach that combined morphometric, molecular, and cladistic evidence from populations in Mexico, the United States, Costa Rica, and India. As a comparative reference in the cladistic analysis, character states from material deposited in the United States National Museum of Natural History were incorporated. We tested the hypothesis that P. latus, traditionally regarded as a cosmopolitan species, constitutes a complex of cryptic evolutionary lineages. Adult mites were collected from different host plants and geographic regions, and their identity was confirmed using specialized taxonomic keys. Twenty-five females and males per population were analyzed, evaluating 17 and 14 morphometric variables, respectively. Data were analyzed using ANOVA and Tukey’s HSD test. Molecular analysis was based on amplification and sequencing of the mitochondrial COI gene. Phylogenetic relationships were inferred using maximum likelihood, and genetic distances were estimated. Species delimitation was assessed using three independent methods (ASAP, ABGD, and bPTP). Additionally, a cladistic analysis under parsimony was conducted using 16 discrete morphological characters to evaluate congruence between morphological and molecular evidence. Morphometric analysis detected significant overall differences among populations in females (F9,144= 3.466; p = 0.000672) and males (F9,190= 7.095; p = 7.74 × 10??). Tukey’s test identified differences in some pairwise comparisons, although without defining consistent morphometric groupings or a clear geographic pattern. In contrast, molecular analysis revealed low genetic distances (<0.02) between Mexico (except Chiapas) and the United States, and high divergence (>0.14) relative to Costa Rica, Chiapas, and India. Phylogenetic inference recovered three well-supported clades: (1) Mexico–United States, (2) Costa Rica, and (3) Chiapas–India. The three delimitation methods consistently recognized three independent evolutionary units. The cladistic analysis yielded a consistency index of 1.0 and a structure congruent with the molecular results; the material described by Lindquist occupied an independent position. The integrative evidence supports the existence of at least three well-defined evolutionary lineages within the P. latus complex, revealing marked geographic structuring and limitations of morphology alone for species delimitation in morphologically conserved mites, with relevant taxonomic and phytosanitary implications.