Muskelin coded by MKLN1 gene participates in signal transduction, cellmatrix adhesion and cellular component movement as an intracellular protein. In previous study, MKLN1 containing 15 repeats of dinucleotide (CT) was identified from a cDNA library of grass carp, Ctenopharyngodon idellus. To further investigate the polymorphism of the dinucleotide, we examined ten individuals from three different grass carp population in this research and identified other different repeats of dinucleotide as (CT)₉、(CT)₁₀、(CT)₁₁ and (CT)₁₃ . Each individual owning at most two loci indicates only one copy MKLN1 in the genome of grass carp. Compared with its orthologure in zebrafish (Danio rerio) or fugu (Takifugu rubripes) genome, the dinucleotide microsatellite was found not in an exon, but in one intron corresponding 10th intron of MKLN1 in Danio rerio or Takifugu rubripes. Further investigation mRNA fragment spanning from 10th to 11th exons showed that there existed mRNA alternative splicing in MKLN1 and the microsatellite was indeed located in unspliced 10th intron in grass carp. Terminal code “TGA” locating in unspliced intron leads the transcript to translate into truncated muskelin. The truncated muskelin might lose partial function because of kelch domain broken. Moreover, the abundance of unspliced transcript was higher than that of spliced transcript in gill, intestine, head kidney, skin, hepatopancreas, muscle and kidney. Taken together, the microsatellite we found in one EST of MKLN1 is from an unspliced intron, and the unspliced intron leads the transcript to encode truncate muskelin.