Information about rare species used for decide widely spectrum of problems. In practice ‒ for estimating environmental impact from human activities. For example by studying biodiversity in fundamental science. This information very important for monitoring and prevention of species extinction. Regional and Federal Red Books serve this aim. However freshwater mollusks species of the Bolshoy Yugan river basin not presented in the Federal Red Book of Russian Federation. In addition, in the Regional Red Books of Khanty-Mansi autonomous region and Tyumen region data about mollusks are absence. This paper the first step to fill in the gap. Article contains the first data about rare species of freshwater mollusks of the Bolshoy Yugan River basin collected during the field season of 2016. In future, these species possibly will be propose to inclusion in the Red Book of Khanty-Mansi autonomous region. I followed the standard techniques of mollusks sampling, fixation and laboratory treatment. In this research I call species rare if species occurrence was 5,0% and lower. I used contemporary macrosystems of mollusks in the level above family groups of both Bivalves and Gastropods. In addition, on the level under family groups and lower I used alternative approach, which consist of combination of two different taxonomic systems: “traditional” European and Ya.I. Starobogatov’s scientific school or “Russian”. The collection of mollusks is kept in the Federal Zapovednik (Nature Reserve) “Yuganskiy”, which was the material base of my study. In the article discussed aspects of rareness and difficulty of investigates freshwater mollusks. These difficulties connected with existence of different taxonomical approaches and underexplored mollusk's fauna and ecology. Studies of rare species in the Western Siberia are briefly considered. The results of own research and annotated list of rare mollusks species of Bolshoy Yugan River basin collected during the field season of 2016 are presented. Showed that significant part of species richness in the Bolshoy Yugan River basin consist of rare species. These results do not change independent of applied taxonomical approaches “traditional” or “Russian” and discussed with facts in malacologycal literature. There are 50 species of freshwater mollusks were find in 2016, 41 of them are rare in the Bolshoy Yugan River basin. In conclusion marked need for further research of freshwater mollusks. In addition denoted some important priorities of studies, such as systematics, fauna, zoogeography and ecology of mollusks. The question about inclusion in the Red Book of Khanty-Mansi autonomous region some any species of freshwater mollusks are still opened. Because needed additional facts about distribution and abundance species from others parts of region.Partial financial support for this study was obtained from the Ministry of Education and Science of Russian Federation (project 6.1352.2017/ПЧ).