To accelerate the molecular analysis of genetics,evolution and behavior, etc. in the honey bee (Apis), the frequency and density of simple sequence repeats (SSRs) have been analyzed from the bee EST (expressed sequence tag) database comprising 15 869 sequences amounting to 7.9 Mb. Results showed that the frequency of SSRs was 1/0.52 kb in bee ESTs, and hexanucleotide repeats (45.0%) motifs appeared to be the most abundant type in bee,the dinucleotide, mononucleotide, trinucleotide, tetranucleotide and pentanucleotide repeats are 17.9%, 14.1%, 11.6%, 9.2% and 2.2%, respectively. Meanwhile, the A-rich repeats are predominant in each type of SSRs, such as A, AT, AG, AC, AAT, AAG, AAC, AAAT, AAAG, AAAAG, AAAAT, AATAT, AAAAAG and AAAAAT repeats, whereas G-rich repeats are rare in the coding regions. The further analysis suggests that, apart from minor deviations, there is no significant difference in the distribution and density of microsatellites in the redundant and non-redundant set of bee ESTs. Furthermore, the availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in bee.