The citrus red mite, Panonychus citri (McGregor), is an economically important pest on citrus. To better understand the population structure of P. citri, we developed 15 novel polymorphic microsatellites derived from expressed sequence tags (EST). The new microsatellites were assessed in 32 female individuals sampled from Quanzhou (Fujian Province), China. The polymorphic information content (PIC) for each locus ranged from 0.305 to 0.726, with an average of 0.491. The number of alleles per locus ranged from 2 to 6, with an average of 3.8. The observed and expected heterozygosities ranged from 0.094 to 0.438 and from 0.345 to 0.764, respectively. Significant linkage disequilibrium was detected for three pairs of loci (PC3 and PC9, PC3 and PC11, PC11 and PC13). Twelve of the 15 loci deviated significantly from Hardy-Weinberg equilibrium (HWE). The presence of null alleles, inbreeding and the Wahlund effect were considered potential sources of the deviations from HWE. The new polymorphic microsatellites provide a valuable resource for future population genetics studies and management of P. citri.