Traditional morphology-based taxonomy of eriophyoid mites (Acari: Eriophyoidea) has been challenged by molecular-based technologies in the detection of cryptic species. However, the implications of such cryptic diversity appear to differ when methods based on different types of data are used. Here, samples of a host-associated eriophyoid mite species, Tetra pinnatifidae, collected from different host plants and localities are evaluated. The congruence of results based on morphometric (32 characters), mitochondrial (16S), and nuclear (28S) data were evaluated and showed a host-associated cryptic diversity dividing this morphospecies into several groups/clades that were morphometrically indistinguishable. In comparison, the 16S data confirmed cryptic speciation and intra-clade host-associated diversity, while 28S did not. In contrast, 28S data revealed potential gene flow between host-associated populations. High mitochondrial divergence, as well as low nuclear and morphological divergence indicated very recent stage of cryptic diversity of this eriophyoid mite.