Composition and distribution of chromatophore on back scales, abdomen scales, and color pattern scales were studied on varieties of carp (Cyprinus carpio) and crucian carp (Carassius auratus) with different body colors. The results showed that the chromatophores on upper layer were melanin, red pigment and yellow pigment, which were distributed on the back area and accounted for 25%-35% of the scale; the main chromatophore on lower layer was guanine, with a little melanin, red pigment and yellow pigment, which were distributed on the proparea and back area, and accounted for 30%-65% of the scale. Based on the analysis, we summarized the differences of chromatophore distribution between varieties with similar body color; discussed the distribution of guanine on carp and crucian carp, the evolution of the body color on one of Carassius auratus variety with red color, and the genetic characteristics of melanin on varieties of carp and crucian carp.