The current study combined a traditional ecotoxicological experimental design with a global gene expression profiling approach to explore the molecular responses of larval Phyllospongia foliascens exposed to water accommodated fractions (WAF) of partially weathered condensate to identify a selection of useful marker genes to use in future assays examining sublethal responses of sponge larvae to hydrocarbons. Additionally, responses of the associated sponge larval microbiome were investigated with a focus on identifying microbial indicator species for high condensate WAF exposures.