INTRODUCTION Lakes are significant resources for the development of any area. They are especially important for the development of human settlements, tourism and recreation, fisheries, and other industries. About 40% of all lakes in Latvia are located in Latgale in the Augszeme Highland. According to the quality indicators, they are clean lakes with low trophic state indexes (Urtane, 1998; Latvijas ezeru, 2002). Salmonid fish lakes are one of the priority water bodies in Latvia. Latgale has a high percentage of lakes that fall into this category; however, there have not been any extensive ecological studies of these lakes in the region. In accordance with the Regulations of the Cabinet of Ministers No. 118, Appendix 2 of 2002 there are 26 salmonid lakes in Latvia. One salmonid species found in these lakes is vendace (Coregonus albula), which is a planktophagous fish. Vendace was found in 30 lakes of Latvia in the 1930s, in 11 lakes in the 1950s-1960s, and only in 5 lakes in the 1990s. This means that this economically important species is gradually disappearing from the Latvian lakes. Since 1995, vendace has been included into the Red Data Book of Latvia as rare species of the 3rd category. Vendace is also included in the lists of the specially protected species. Since vendace mainly feeds on zooplankton, we chose zooplankton as a major research object for our paper. Zooplankton (e.g. Cladocera) is an important feeding base for juvenile fish and planktophagous fishes such as salmonids (Hebert, 1982; Malone & McQueen, 1983; Pinel-Alloul, 1995; Cimdins, 2001; Wetzel, 2001; Chang & Hanazato, 2004) and plays an essential role in the transformation of substances and energy in water bodies. Zooplankton controls the number of bacteria and algae, contributing to the biological self-purification process of water. A zooplankton community is a dynamic system in which the species composition may change significantly during the season. Temporal changes of the zooplankton species found in temperate lakes are influenced by many factors, including temperature, food, competition, and predation (Hebert, 1982; Malone & McQueen, 1983; Dodson, 1984; Larsson & Dodson, 1993; Weider & Pijanowska, 1993; Pinel-Alloul, 1995; Cimdins, 2001; Wetzel, 2001; Chang & Hanazato, 2004; Harris et al., 2012). It is a well-known fact that zooplankton organisms are very sensitive to the biotic and abiotic influences, which lead to structural and functional changes on a polymorphism level (De Meester et al., 1995). This makes them good bioindicators for the evaluation of water quality and toxicity as well as for experimental purposes in ecology and genetics (Sloka, 1998; Dussart & Defaye, 2001). During our research (Brakovska & Skute, 2007, 2009; Brakovska & Paidere, 2012; Brakovska et al., 2012; Jurevics et al., 2012) we found that Daphnia cucullata is among dominants in the Cladoceran community of Latvian salmonid lakes. It forms also an important part of the vendace food (Viljanen, 1983; Sutela & Huusko, 1997). Therefore we have decided to study for the first time in Latvia the genetic diversity and plasticity of D. cucullata in Latvian salmonid lakes as so far the investigations of zooplankton species in Latvian lakes have been based only on morphology. Cladocera genera (e.g. Daphnia) have frequently been used as model organisms for ecological genetic research for more than 150 years (e.g. Lubbock, 1857; Colbourne & Hebert, 1996; Harris et al., 2012). It should be noted that Daphnia as a model organism is also used in other scientific disciplines, including chemistry and physiology. Thanks to Winfried Lampert and his colleagues all around the world, Daphnia has become a model organism in the international freshwater ecology (Larsson & Weider, 1995; Lampert, 2006). Daphnia has also been used in studies of the predator-induced polyphemism (Ebert, 2005; Stollewerk, 2010). …