Microsatellite is a genetic marker, explored recently. In order to improve related studies on genetics of Anopheles gambiae, simple sequence repeats of the entire mosquito genome with 1~6 bp nucleotide motifs were analyzed. Abundance and distribution of microsatellites across the A.gambiae genome were analyzed and compared between various (exons, introns and intergenic) regions of all the chromosomes. About 2.14% of the mosquito genome was occupied by SSRs. Chromosome X had the maximum density of SSRs. Abundance of A repeats was similar to C repeats. AC was a little more than two times as abundant much as AG. However, AT and CG repeats were rare. For tri-and tetramer repeats, AGC, AAAC and AAAT predominated while ACG, ACT, AGG, CCG, ATGC, CCCG, ACTG, AACT, ACGT, AGAT, CCGG, ACCT and AGCT were rare. For some pentamer repeats, one was completely absent on a certain chromosome, even on several chromosomes. SSRs in exons of all chromosomes were less abundant than in introns and intergenic regions except for mono- and dimer repeats in exons of chromosome 2L. Abundance and distribution of SSRs on the two arms of each chromosome showed much in common.