The major histocompatibility complex (MHC) class I α₂domain was used to study the genetic variation among Yangtze River Laojianghe (YZL) , introduced Danube River (DAN) and Mississippi River (MIS) populations of silver carp (Hypophthalmichthys molitrix). A total of 68 different nucleotide sequences were got from 117 clones in 40 individuals of the three populations. The major results were as follows: （1）21, 27 and 20 alleles were detected in the YZL, DAN and MIS populations respectively and the wide range of nucleotide (54.1%-99.5%) /amino acid (39.4%-98.6%) sequence similarities indicated relatively high polymorphism of MHC class I α₂ domain of silver carp in the three populations. （2） The range of mean nucleotide /amino acid sequence similarities was MIS > DAN > YZL, but on the contrary, the nucleotide /amino acid diversity index (π/π_aa) was YZL > DAN > MIS. So, it was concluded that YZL population had higher variation than the other two populations. （3） The AMOVA results ,based on the amino acid sequences, indicated that there existed significant genetic differentiation whether among the three populations or between native and introduced populations (P<0.05). （4） The ω values of non synonymous /synonymous nucleotide substitution were YZL（1.652 5）> MIS（1.499 5） > DAN（1.337 0）> 1, and five positive selection sites were detected in the peptide binding region (PBR), indicating positive selection pressure on the three MHC class I α₂ domain of silver carp with the highest selection pressure on the YZL population.