Environmental contaminants pose a significant selection pressure across taxa potentiating evolved resistance to chemicals. However rapid evolution may alter molecular and physiological homeostasis leading to trade-offs. To elucidate molecular underpinnings of evolved chemical resistance we compared liver gene expression and methylation profiles in polycyclic aromatic hydrocarbon (PAH)-adapted Atlantic killifish (Fundulus heteroclitus) in the Republic site (RP) Elizabeth River Virginia with PAH-sensitive Kings Creek (KC) fish. Data herein include alternatively spliced genes differentially expressed genes methylation mRNA read counts sequenced RRBS and gene ontologies.