The complete 12S rRNA genes from the five F11 allotetraploids, two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, and one Japanese crucian carp were successfully cloned and sequenced. Sequence compositions and variations were analyzed with MEGA 1.0 software. Five F11 allotetraploids shared two haplotypes, and two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, one Japanese crucian carp shared one haplotype, respectively. The similarities among red crucian carp, xiangjiang common carp, allotetraploid, diploid gynogen, Japanese crucian carp, and triploid crucian carp varied from 95% to 99%. The similarities between allotetraploid, triploid crucian carp and their female parents (red crucian carp and Japanese crucian carp, respectively) were higher than those between allotetraploid, triploid crucian carp and their male parents (xiangjiang common carp and allotetraploid, respectively). Such result indicated that mitochondrial 12S rRNA genes of the allotetraploid and triploid crucian carp were inherited maternally. A phylogenetic tree was reconstructed using the neighbor joining method of the MEGA package. It was noticeable that after nine generations from F3 to F11 hybrids, the five F11 allotetraploids shared two haplotypes (AT-1 and AT-2), indicating the allotetraploid stock had the genetic diversity. The results provided some valuable information for the breeding, genetic conservation, and population rejuvenation of the tetraploid stock.