Insect pathogenic fungi (IPF) differ widely in their capability to infect different hosts. Some are generalists and will, given a sufficient number of infectious spores are present, infect almost any species of insect (e.g. Hypocrealean Metarhizium and Beauveria). Members of a different main IPF phylum Entomophthoromycota generally have more narrow host-ranges where some species for example only infect aphids or only locusts. Certain species (or strains) are even more host specific and are only known to infect a single or very few taxonomically related insect species under natural conditions (e.g. Entomophthora, Strongwellsea and Entomophaga). Species diversification of the obligate IPF within Entomophthoromycota thus seems to be primarily driven by co-evolutionary host adaptation to specific insect families, genera or species-complexes, but the underlying genetic factors of host adaptation in this fungal order are largely unknown and leave many unanswered questions. For example are the number of virulence factors increasing, or decreasing when fungal pathogens adapt to a narrow range of potential hosts? And, are host specialization based on many genetic changes with small effect or few with large effect? Here we examine closely related species within the Entomophthora muscae species complex: E. muscae s. str. infecting the common housefly Musca domestica and E. muscae s.l. strains infecting the cabbage fly Delia radicum. We use RNA-seq based comparative transcriptomics to unravel genetic differences and similarities in order to detect patterns of host-specific molecular adaptation.