Ostracod crustaceans are among the most abundant microfossil animals. Understanding intra- and interspecific variability of their shell is of pivotal importance for the interpretation of paleontological data. In comparison to appendages, ostracod shell displays more intraspecific variability (in shape, size, and ornamentation), often as a response to environmental conditions. Shell variability has been studied with sophisticated methods, such as geometric morphometrics (GM), but the conspecificity of examined specimens and populations was never tested. In addition, there are no GM studies of appendages. We build on previously published high cytochrome c oxidase subunit I (COI) divergence rates among populations of a brackish water species, Ishizakiella miurensis (Hanai, 1957). With landmark-based GM analyses of its shell and appendages, and additional genetic markers (ITS, 28S, 18S), we test if the genetic variability is structured in morphospace. This approach is the core of integrative taxonomy paradigm which has been proposed to bring the gap between traditional taxonomy and other disciplines such as evolutionary biology. The results show that it is the shell shape, and not the shape of appendages, that mirrors the molecular phylogeny, and we describe a new species. Our results suggest that the landmark-based GM studies may be useful in paleontological datasets for closely related species delineation. We implement molecular clock and population statistics to discuss speciation processes and phylogeography of the two congeners in Korea and Japan.