Abstract: In aquaculture practice, some rice flower carp were found to have softened bones, and their intermuscular bones became imperceptible after steaming or boiling. These fish are referred to as soft-bone rice flower carp. To investigate the causes of this condition and to establish a rapid in vivo method for identifying soft-bone individuals, we collected scales from soft-bone and hard-bone rice flower carp with body mass ranging from 80 to 120 g. We analyzed and compared the morphological traits, calcification level, hardness, and nutritional composition of the scales between the two groups using measurement, alizarin red staining, texture analysis, as well as composition determination. The results show that the average area-to-thickness ratio of the five scales on the upper part of the lateral line was exceptionally significantly higher in the soft-bone group than in the hard-bone group (p<0.000 1). The scale calcification level of the soft-bone group was very significant lower than that of the hard-bone group (p<0.01). In both groups, the hardness of scales from different body regions followed the same order: dorsal scales>caudal scales>ventral scales, and the scale hardness in each region was significantly lower in the soft-bone group than in the corresponding region of the hard-bone group (p<0.05). The contents of crude protein, amino acids, and collagen in the scales of the soft-bone group were extremely significantly higher than those in the hard-bone group (p<0.001), while the contents of ash, calcium, and phosphorus were extremely significantly lower in the hard-bone group (p<0.001). Based on these findings, we established a rapid in vivo identification method for soft-bone rice flower carp by measuring the scale area-to-thickness ratio. This study not only elucidates the biological characteristics of scales in soft-bone rice flower carp and explores possible causes of the soft-bone condition, but also provides a rapid in vivo identification method for soft-bone rice flower carp.