Understanding how host phylogeography shapes parasite assemblages is fundamental to evolutionary ecology. We used Carollia perspicillata, a widespread Neotropical bat with two well–defined mitochondrial clades, to test whether genetic divergence predicts the beta diversity of its obligate streblid ectoparasitic flies. A systematic review of 52 articles produced a data set (2000–2024) encompassing 58 localities from Mexico to Argentina and recording 15 fly species primarily associated with C. perspicillata. For each site we compiled mean-abundance and incidence matrices and partitioned Bray–Curtis ( \(\:{\beta}_{BC}\) ) and Sørensen ( \(\:{\beta}_{Sor}\) ) multiple-site dissimilarities into balanced variation/turnover ( \(\:{\beta}_{BC.BAL}\) and \(\:{\beta}_{Sim}\) ) and gradient/nestedness components ( \(\:{\beta}_{BC.GRA}\) and \(\:{\beta}_{SNE}\) ). Total beta diversity was high (both \(\:{\beta}_{BC}\) and \(\:{\beta}_{Sor}\) were 0.92), driven mainly by species replacement ( \(\:{\beta}_{BC.BAL}\) = 0.89; \(\:{\beta}_{Sim}\) = 0.79). Nonmetric multidimensional scaling (NMDS) analysis showed an overlap in the species composition of ectoparasitic flies between the Widespread and Southeast host clades of C. perspicillata, however PERMANOVA showed that beta diversity was significantly different between the host’s phylogenetic groups. Generalized Dissimilarity Models (GDM) explained up to 20% of deviance in abundance–based \(\:\beta\:\) –diversity using five predictors and 10% in incidence-based \(\:\beta\:\) –diversity using three predictors. \(\:{\:F}_{st}\:\) alone accounted for the largest proportion of explained deviance across all models, underscoring host genetic divergence as the principal driver of flies’ species turnover. Temperature seasonality and the composition of sympatric bat-fly networks exerted secondary effects, whereas geographic distance and precipitation contributed little. Our results demonstrate that historical processes embedded in host phylogeography impose strong constraints on ectoparasitic community assembly, while local biotic interactions and climate modulate patterns at finer scales. Integrating evolutionary and ecological filters is therefore essential to fully understand host-parasite dynamics.