L.) was investigated in three populations (Ulungur Lake, Jili Lake and No.6 Lake) in Xingjiang, China and one population (Balaton Lake) in Hungary by using 18 microsatellite markers. The results indicated that the mean allele richness (<0.05), whereas the mean inbreeding coefficient (of the Hungarian population was higher than that of the Chinese populations. Significant bottleneck signal was detected from Hungarian population by using SMM and TPM model (ST values indicated that <0.01). The results of Neighbour-joining tree, Principal Coordinate Analysis (PCA) further confirmed that there was obvious genetic difference between Chinese and Hungarian populations. Furthermore, the results of Bayesian cluster analysis showed that northern pikes in the Lake rather than from the Jili Lake.