With their power to shape animal morphology, few genes have captured the imagination of biologists as much as the evolutionarily conserved members of the Hox clusters. Hox genes encode transcription factors that play a key role in specifying the body plan in metazoans and are therefore essential in explaining patterns of evolutionary diversity. While each Hox cluster contains the same genes among the different mammalian species, this does not happen in ray-finned fish, in which both the number and organization of Hox genes and even Hox clusters are variable. Teleost fishes provide the first unambiguous support for ancient whole-genome duplication (third round) in an animal lineage. The number of genes differs in each cluster as a result of increased freedom to mutate after duplication. This has also allowed them to diverge and to adopt novel developmental roles. In this review, the authors have firstly focused on broadly outlining the duplication of Hoxgenes in fishes and discussing how comparative genomics is elucidating the molecular changes associated with the evolution of Hox genes expression and developmental function in the teleost fishes.Additional related research aspects, such as imaging of roles of microRNAs, chromatin regulation and evolutionary findings are also discussed.