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Gibel carp, Carassius auratus gibelio Bloch, as a subspecies of Carassius auratus, has a wide geographic distribution from northern Europe to Asia. As a new culture target, it has been used widely for aquaculture practice in recent 30 years in China, and its production capacity has increased up to 2 billion kilograms annually. Gibel carp possess several interesting characteristics: 1) It is a triploid fish with more than 150 chromosomes, 2) It exists as a bisexual population with predominantly more females (an 80 : 20 female: male ratio) in natural habitats, 3) It has dual reproductive modes of gynogenesis and bisexual reproduction, 4) Various gynogenetic clones have been identified. These features make gibel carp a promising study model for evolutionary genetics, developmental biology and selective breeding. Recently, we have detected clonal diversity of gibel carp in Fangzheng stock hatchery of Heilongjiang Province and Qihe stock hatchery of Henan Province. Up to now, however, little information had been known about the status of gibel carp populations from the Irtysh River water system in Xinjiang Province. In order to obtain a better understanding of the status of clonal diversity of the gibel carp populations, four populations of Carassius auratus were collected from the Irtysh River water system in this study. Flow cytometry was applied to analyze their blood cells, revealing that all of them were triploid gibel carp. Then, a total of eight different clones were clearly discriminated from these gibel carp populations by analysis of serum transferrin phenotypes. Among them, four clones were identical to those identified previously, whereas, the other four were new. Clones A and M were the most wide-ranging, occurring in all of the four populations. Clone J appeared in two populations. Each of the other five clones was specific to single population. These distribution patterns of different clones within populations might reflect clones being able to migrate and differences in viability of a clone among different water bodies. Among these sampled populations of gibel carp, one had the level of clonal diversity obviously lower than those in the other tree, similar to those in populations reported, probably suggesting negative effects of human activities such as hydraulic engineering construction and overharvesting. The clonal diversity revealed in this study will likely benefit evolutionary genetics and selective breeding studies. At the same time, this work also highlights the significance of protecting clonal diversity Of gibel carp in the Irtysh River water system.