The present paper is to investigate gene distribution at different genomic region with different local GC content. With shout-gun technology, we sequencing two sequences at 3p25.1 and 3p26.1, at genome size 328 kb and 753 kb respectively. The 328 kb sequence,with an average GC content as high as 47.57%, has high gene density (13.7 gene/100 kb). However, another sequence at 3p26.1 only includes one exon and one intron of large gene GRM7 and the coding sequence size is 11 520 bp only taking a small part (1.31%) of the whole genome region. High percentage distribution of GC-rich repeats of SINEs explain high GC genomic region at 3p25.1 and high concentration of AT-rich repeats of LINEs at 3p26.1 lead to low GC content of the region. Our results suggest isochore structure is the result of coevolution between gene and genome.