Background The reconstruction of phylogenetic relationships for allopolyploids using genomic data is challenging because hybridization and polyploidy can blur history. In cyprinids, one allopolyploidization event involves goldfish and common carp, yet little is known about the origins of other cyprinid polyploid lineages, including their maternal and paternal ancestral lineages. Results Herein we employ 10 HOX genes, genomic and transcriptomic data of representative species from seven subfamilies in Cyprinidae to investigate the origins of polyploid lineages. Analyses of the nuclear and mitochondria genomes reveal that the Schizothoracinae and Cyprininae share the same maternal common ancestor, and identify the candidate genes for identifying maternal gene-copies from Cyprininae. Gene-trees show a close relationship between Sinocyclocheilus grahami and Cyprininae, and indicate that they share the same whole genome duplication (WGD) event about 12.10 ~ 14.03 Ma. Another allopolyploidization event involves Torinae; one duplication clustering with Schizothoracinae and Schizopygopsinae identifies them as paternal siblings. Further, Labeoninae has a history of recurrent hybridization, which is supported by both gene-trees from genomes and HOX genes. Conclusions Collectively, the diverse WGD history makes Cyprinidae a candidate system for investigating the origin of hybridization and polyploidization in vertebrates. Further investigations should enlarge the representatives, combine morphological traits, and reconstruct gene-trees based on whole-genome markers.