[Background] The chive gnat, Bradysia odoriphaga Yang and Zhang (Diptera:Sciaridae), is a severe agricultural pest in China. Knowledge on the biology, dispersal, and other important aspects of this insect is limited. Filling this knowledge gap is hampered by the lack of suitable the genetic markers. The aim of the present study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) that can be used for genetic diversity and structure analysis of B. odoriphaga.[Method] The SSRs primers were designed and tested based on the ESTs of B. odoriphaga obtained in this study.[Result] A total of 3383 SSRs were identified from 42095 unigenes. Sixteen pairs of primers were designed and tested in 30 B. odoriphaga larvae, of which nine primer pairs produced polymorphic amplicons. Thirty alleles were identified from 30 larvae using the nine markers, with an av-erage of 3.33 alleles per locus (ranged from 3 to 4). The range of observed and expected heterozygosity was 0.0000~0.6875 and 0.0370~0.6877, respectively. Five of the nine loci exhibited significant departure from Hardy-Weinberg equilibrium.[Conclusion and significance] The nine polymorphic microsatellite loci developed in this study can be used to research the genetic diversity and structure of B. odoriphaga populations.