Previous reports involving mammalian systems, particularly mice, have demonstrated the existence of cis- and trans-acting modifiers of transgene methylation. These modifiers are thought to be important in dominance modification, genome imprinting and cellular expression mosaicism. Their potential role in the penetrance and severity of many complex human diseases could be of even greater significance. In the present investigation we demonstrate that modifiers that act in a similar fashion to those identified in mice also exist in a non-mammalian vertebrate, the zebrafish Danio rerio. We also provide evidence that the transgene methylation pattern may be influenced by the sex of the individual and environmental modulators such as temperature and sodium butyrate. These data support the theory that this type of dominance modification is mechanistically similar to position effect variegation in Drosophila. Furthermore, these data suggest evolutionary conservation of the modifiers, at least within vertebrates, and imply that they and their actions are important in normal vertebrate development.