An integrative taxonomy based on traditional morphological method, molecular systematics and geometric morphometrics was tested to identify two species of torrenticolid mites, which are similar in morphology. A new species of the water mite genus Torrenticola from China, T. nipponicella Gu & Guo sp. nov., was described and illustrated in this paper. The descriptions included morphological features, molecular data, geometric morphometric data, and a discussion of their taxonomic status and integrative taxonomy. Meanwhile, some potential taxonomic characters of those species were analyzed by canonical variate analysis and principal component analysis. Those analyses of two landmark configurations revealed important taxonomical characters in dorsal (dorsoglandularia 1–3) and ventral shields (coxoglandularia 2, 4, ventroglandularia 3).