Significance Divergent lineages can respond to common environmental factors through convergent processes involving shared genomic components or pathways, but the molecular mechanisms are poorly understood. Here, we provide genomic resources and insights into the evolution of mammalian lineages adapting to aquatic life. Our data suggest convergent evolution, for example, in association with thermoregulation through genes associated with a surface heat barrier ( NFIA ) and internal heat exchange ( SEMA3E ). Combined with the support of previous reports showing that the UCP1 locus has been lost in many marine mammals independently, our results suggest that the thermostatic strategy of marine mammals shifted from enhancing heat production to limiting heat loss.