Following the many years of studies conducted on Dniester and Prut Rivers ichtyofauna (Moldova’s territorial limits) it became possible to elucidate the comparative aspects between these two large water macroecosystems (Bulat et al., 2014). Although the Danube basin (which includes Prut River) and Dniester are separated by geographic barrier of Black Sea, their ichtyofauna have many common points, but the differences become clearer only in the current intensification of anthropogenic pressure. High similarity of ichtyofauna of these two hydrographic basins is due to the shallow continental shelf between the Danube mouths and Dniester estuary, which shows that during the glacial period Dniester River, was a tributary of the Lower PaleoDanube (Serban, Bănărescu, 1985). Therefore, at the moment, we found the following comparative particularities of ichtyofauna between Dniester and Prut Rivers (Moldova’s territorial limits): 1. Active processes of limnophilous, silting and eutrophication of the Dniester River ecosystem as a result of multiple fragmentations, has led to substantial expansion seaside area, characterized by large areas of shallow water, rich in aquatic vegetation. This has become particularly attractive habitat for euritope opportunistic species with short and medium life cycle (Alburnus alburnus, Rutilus rutilus, Rhodeus amarus, species of gobies, Cobitis complex, Carassius s. lato, Syngnathus abaster, etc.), where they have found favorable place for nutrition, reproduction and refuge. Unlike Dniester River, coastal areas of the Prut riverbed is characterized mostly by steep banks, poor in aquatic vegetation and flowing faster water, and transparency which is a feature for low water of Prut River becomes an additional cause of decreasing the primary production of ecosystem, and thus on the secondary one (Ungureanu, 2014). 2. As concerning the diversity and share in the catches of fish species with different rarity status (Vimba vimba, Ballerus sapa, Pelecus cultratus, Leuciscus idus, Zingel zingel, Zingel streber, Alburnoides bipunctatus, Barbus petenyi, Lota lota, Sabanejewia balcanica, etc.), Prut River significantly outcompete Dniester River, which indicates a higher anthropogenic pressure on river ecosystem. 3. Greater abundance of Gymnocephalus cernua in Costesti–Stica reservoir, and including some of rheophyls species as: Barbus barbus, Vimba vimba, Squalius cephalus, Chondrostoma nasus, Ballerus sapa, etc., involves a more favorable ecological status of this anthropic aquatic ecosystem compared to Dubasari accumulation on Dniester River (Bulat, Davideanu, 2016). 4. Ichtyofauna of Dniester River is more affected by interventing species abundance than in Prut River: the species of gobies, Syngnathus abaster, Gasterosteus aculeatus, Pungitius platygaster, Clupeonell acultriventris, Atherina boyeri etc. The determining factors of active pontisation of Dniester ichtyofauna, serve anthropogenic negative processes of hydrobiotopic alteration, and, not least, the fish overexploitation with selective effect (causing undermining of trophic level of ichtyophagous and top large competitors, naturally serving as a force major regulatory in ecosystem). 5. From the native fish species of Cobitis complex is well represented in Dniester River ichtyofauna than in Prut River (except Sabanejewia balcanica) while Gymnocephalus complex (Gymnocephalus cernua, Gymnocephalus baloni and their interspecific hybrids) is better represented in Prut River (except Gymnocephalus acerina). Acknowledgment: The study was performed within the national project 15.817.02.27A