Grass carp is one of the most important freshwater aquaculture fish in China. Though a few molecular markers had been reported, it was not enough for grass carp germplasm improvement and protection. In order to verify the effectiveness and practicability of insert/deletion mutations reported in grass carp genome, 85 insert/deletion mutations were randomly selected and analyzed. After simple sequence analysis and attempting primer design, 49 markers were removed due to being simple sequence repeats or unable to design primer for them. Finally, 36 insert/deletion mutations were successfully characterized by STR genotyping method in 32 wild grass carp (collected from Pearl River). The mean effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) were 1.4976, 0.3190, 0.2970 and 0.2349, respectively. Among all the 36 insert/deletion mutations, three deviated significantly from Hardy–Weinberg equilibrium (P < 0.05). In addition, three pairs of loci (ID-13F with ID-24H, ID-20F with ID-21H and ID-39F with ID-64H) had significant linkage disequilibrium (P < 0.05). Those insert/deletion mutations may lay the foundation for germplasm improvement and protection in grass carp.