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Background  Allotetraploid F 1  hybrids (4nF 1 ) (AABB, 4n = 148) were generated from the distant hybridization of  Carassius auratus  red var. (RCC) (AA, 2n = 100) (♀) ×  Megalobrama amblycephala  (BSB) (BB, 2n = 48) (♂). It has been reported that  Hox  gene clusters are highly conserved among plants and vertebrates. In this study, we investigated the genomic organization of  Hox  gene clusters in the allotetraploid F 1  hybrids and their parents to investigate the polyploidization process.    Results  There were three copies of  Hox  genes in the 4nF 1  hybrids, two copies in RCC and one copy in BSB. In addition, obvious variation and pseudogenization were observed in some  Hox  genes from 4nF 1.Conclusion  Our results reveal the influence of polyploidization on the organization and evolution of  Hox  gene clusters in fish and also clarify some aspects of vertebrate genome evolution.    Electronic supplementary material  The online version of this article (10.1186/s12863-017-0550-2) contains supplementary material, which is available to authorized users.

Hox genes reveal genomic DNA variation in tetraploid hybrids derived from Carassius auratus red var. (female) × Megalobrama amblycephala (male)