We applied 2 methods of phylogenetic regionalization (evoregions and phyloregions) for the distributions of fleas and their rodent hosts across Mongolia. We investigated the congruence between these 2 regionalization schemes and their alignment with physiographic and ecological subdivisions of Mongolia. We identified evoregions and phyloregions for both fleas and hosts. Ancestral regional distributions were reconstructed, and a phylogenetic correspondence analysis identified key contributing lineages. Using the V-measure, we tested for the congruence between (a) evoregions or phyloregions identified for fleas and evoregions or phyloregions, respectively, identified for their hosts and (b) evoregions and phyloregions identified for either fleas or hosts and each of the physiographic/ecological regionalization schemes of Mongolia. Four evoregions and 8 phyloregions were identified for both fleas and hosts, exhibiting distinct spatial patterns. Host-parasite regionalizations demonstrated moderate spatial similarity (V-measure 0.49–0.50), a significantly higher congruence than previously reported at the larger Palearctic scale (0.33). Flea regionalizations exhibited stronger congruence with environmental schemes than did host regionalizations. We concluded that evoregionalization and phyloregionalization capture distinct evolutionary signals, reflecting the role of in situ diversification vs. phylogenetic turnover resulting from dispersal. Host-parasite co-regionalization is scale-dependent, with increased congruence at regional scales. Despite adult fleas’ obligate host dependence, their regionalization is not merely a passive reflection of host biogeography but is also profoundly shaped by environmental conditions. These findings emphasize the importance of method choice, scale and eco-evolutionary interactions in shaping complex biogeographic patterns.