Pores and sensilla on ostracod shell have often been used in studies of ontogeny, taxonomy, and phylogeny of the group. However, an analysis of sexual dimorphism and variation between valves in the number and distribution of pores is lacking. Also, such studies have never been done on a widely distributed, morphologically variable, and weakly ornamented freshwater ostracod. Here, we survey pores in one such species, Physocypria kraepelini. We choose 27 homologous pores as landmarks for 2D-geometric morphometric analysis, with the aim to assess intersexual and between valves variation in size and shape relative to the Fourier outline analysis. This species has only simple (Type A) pores with and without a lip, and each pore carries an undivided sensory seta. Our results show that the total number of pores varies (from 270 to 296), but this is not associated with a specific valve. Males carry fewer pores than females, however no sex specific pores are found. Small intrapopulation divergence of the Cyt b molecular marker (1%) indicates that morphological variability is not species related. We found that P. kraepelini exhibits directional asymmetry of size and shape, sexual size dimorphism (SSD) but lacks sexual shape dimorphism (SShD). Two geometric morphometrics methods were congruent in the estimation of SSD, SShD, and directional asymmetry of shape but differ in the statistical evaluation of directional asymmetry of size. Contrary to other animal groups, our study suggests that ostracods have more pronounced directional asymmetry of shape compared to directional asymmetry of size.