The objective was to document the variations in the intermuscular bone counts among three carp strains: mirror carp, hybrid carp [Boshi carp (Cyprinus pellegrini) × Heilongjiang carp (Cyprinus carpio)], and a cold-resistant strain of Hebao carp. The intermuscular bone counts, lengths, and weights were obtained from 146 fish; the bone count ranged from 55 to 110 (mean 92.85) among the three strains. Mirror carp had the lowest number of intermuscular bones and a higher coefficient of variation in counts relative to the other two species. There was no relationship between the intermuscular bone counts to standard length or body length. Similarly, there was no difference in the intermuscular bone count or shape between the left and right sides of the body. However, the count was significantly higher (P < 0.01) in the anterior region (snout to cloaca: 54% of the total count) than in the posterior region (cloaca to base of caudal fin: 46% of the total count). There was a significant difference between strains (P < 0.0001), but not between age classes; a significant difference was also observed in the posterior region counts among strains, but not in the anterior region (P < 0.0001). Similarly, the difference in counts in the posterior region was primarily related to differences in the counts of three of the six types: non-forked (I), tree-branch and two-end-bi-fork type. Our results suggest that selective breeding protocols should target a reduction in the number of intermuscular bones in the posterior region, particularly in mirror carp.