The Montara incident which occurred in 2009 in the Timor Sea, resulted in the release of an estimated 23,000 barrels of oil and gas condensate over 74 days. Following the operational response, the scientific monitoring focussed on commercially important fish in order to ascertain the suitability for human consumption, as well as inform on the long term effects of the oil spill on fish health. Red emperor (Lutjanus sebae, n = 807) and glodband snapper (Pristipomoides multidens, n = 1531) were sampled over 2 years flowing the accidental release, and biopsies collected. A suite of physiological indices (condition factor, liver somatic index and the gonadosomatic index), biomarkers (EROD activity, biliary polycyclic aromatic hydrocarbon (PAH) metabolites, liver integrity measured by serum sorbitol dehydrogenase activity (SDH), oxidative DNA damage) were measured. While fish initially showed signs of exposure to petroleum hydrocarbons, biomarker of exposure in fish collected in the most impacted area have returned to reference levels within 24 months. Only liver somatic index in fish collected at the spill site remained elevated two years after the spill, relative to fish from other locations. Two years of monitoring following the oil spill in a tropical open sea provided information on biomarker tools that are suited to short-term, or long-term monitoring of effects from discharged light crude oil.