Size and nucleotide polymorphisms of intron 2 of the growth hormone (GH) gene was studied in 82 individuals from Takifugu obscurus, Takifugu rubripes and Takifugu niphobles with PAGE, SSCP and cloning. Results showed that there were nine length variants (A~I) in these fishes, ranging from 271351 bp, with a frequency of variation of 24.22%. Sequence analysis of the 9 length variants showed the average percentages of the four bases (ATG and C) were 17.15, 20.77, 37.38 and 24.70, respectively, and the difference between GC content (45.47) and AT content (54.53) was not remarkable. Length variation was mainly due to the variable number of microsatellite TCTG repeats (N=20 approximately 40). Further sequence comparison revealed 4 substitution sites: a (C-->A) transversion at nucleotide 103 and 3 transitions 83(C-->T), 101(A-->G) and 296(G-->A), respectively. Phylogenetic analysis of these length variants placed DD and II into one group first, which was subsequently joined by GG and AA, BB and CC, EE and HH were then clustered together, FF was joined last. Thus, intraspecific variations were much smaller than interspecific variations for the intron 2 of the GH gene.