Benthic diatoms survey was conducted at near shore area (S = 0.4 km(2)) nearby Mouth of river Belbek, SW Crimea, Black Sea. Totally 60 samples (10 sampling sites by 6 replicates per each one) were collected in November 2009 on sandy-muddy substrate within the depth range 6-18 m. At total, 267 species were registered by results of cell calculations in Goryaev counting chamber and microscoping of permanent slides. The most abundant diatoms which were enumerated in the counting chambers (common species) represented on the average 50.2 % of the total species richness (26.0-74.4 % depending on the certain sampling site). The expected species richness (S-exp) resulted by 4 estimators (Jack-knife-1 and -2, Chao-2 and Karakassis-S-infinity) was calculated. The method S-infinity had shown the S-exp results (295 species), that was about 10 % larger than the observed species number (S-obs = 267). Other estimators more considerably overestimated (as large as 32-47 %) the 5(obs) value. The relationship between number of samples (X) and number of observed species (Y) was described by the equation: Y = 75.76 ln(x) + 87.533. This cumulative curve did not attain a horizontal asymptote; the recorded total number of diatom species (267) implied to be considerably lower than the expected species richness. The site-related differences in the total number of common species (S-com), their abundance (N-com), rarefaction index ES(n) and diversity indices (Shannon, Pielou, Margalef) averaged from 6 replicates for each site were compared. Environmental heterogeneity of habitats was found to determine species structure and micro-distribution pattern of the diatom assemblage. The significance of difference in species similarity between any pair of 6 replicates from one sample and between randomly taken replicates from two different samples was assessed by 1-way ANOSLM test. The average similarity of the diatom species composition by replicates from one site was 1.6-2.5 times higher than average similarity by pairwise comparison of replicates from 10 different sites. The obtained results proved the significant differences in the species structure between the adjacent sampling sites caused by variation in key environmental factors important for benthic diatoms, along with the absence of significant differences between replicates randomly taken from one sampling site.