<p>Structural variants such as chromosomal rearrangements and gene duplications can play an important role in the adaptation and diversification of organisms. Here, we used comparative genomics to study the functional implications of structural variants across two families of flies. We compared the reference genomes of eight Asilidae species and six Stratiomyidae species, including the black soldier fly (<i>Hermetia illucens</i>), a species with an ability to convert organic waste into biomass and a recently expanded global range. Our results show that the genomes of Stratiomyidae are generally larger than Asilidae and contain a higher proportion of transposable elements, many of which are recently expanded. Gene families showing more gene duplications are enriched for life history related functions such as metabolism in Stratiomyidae which are known to be active decomposers, and longevity in Asilidae which are predators and have generally longer lifespan than Stratiomyidae. Gene families showing more gene duplications that are specific to <i>H. illucens</i> are mostly related to olfactory and immune responses, while across the Stratiomyidae there is enrichment of digestive and metabolic functions such as proteolysis, providing an explanation for the higher decomposing efficiency and adaptive ability of <i>H. illucens</i> compared to other Stratiomyidae species in decomposing environments. Together, our results shed light on the contribution of structural variants to functional adaptation and gene family expansions that have likely played a role in the ecological success of the black soldier fly.</p>