Using a panel of genes stimulated by oil exposure in a laboratory study, we evaluated gene transcription in blood leukocytes sampled from sea otters captured from 2006-2012 in western Prince William Sound (WPWS), Alaska, 17-23 years after the 1989 Exxon Valdez oil spill (EVOS). We compared WPWS sea otters to reference populations (not affected by the EVOS) from the Alaska Peninsula (2009), Katmai National Park and Preserve (2009), Clam Lagoon at Adak Island (2012), Kodiak Island (2005) and captive sea otters in aquaria. Statistically, sea otter gene transcript profiles separated into three distinct clusters: Cluster 1, Kodiak and WPWS 2006-2008 (higher relative transcription); Cluster 2, Clam Lagoon and WPWS 2010-2012 (lower relative transcription); and Cluster 3, Alaska Peninsula, Katmai and captive sea otters (intermediate relative transcription). The lower transcription of the aryl hydrocarbon receptor (AHR), an established biomarker for hydrocarbon exposure, in WPWS 2010-2012 compared to earlier samples from WPWS is consistent with declining hydrocarbon exposure, but the pattern of overall low levels of transcription seen in WPWS 2010-2012 could be related to other factors, such as food limitation, pathogens or injury, and may indicate an inability to mount effective responses to stressors. Decreased transcriptional response across the entire gene panel precludes the evaluation of whether or not individual sea otters show signs of exposure to lingering oil. However, related studies on sea otter demographics indicate that by 2012, the sea otter population in WPWS had recovered, which indicates diminishing oil exposure.hydrocarbons has the potential to cause not only catastrophic short-term effects, but importantly, often overlooked, long-term damage to individuals, populations or even ecosystems [1,13]. The extent and duration of long-term effects are difficult to assess, as pathophysiological changes within an individual may be significant yet subtle and, consequently, undetectable using classical wildlife diagnostic methods. Alterations in the levels of gene transcription can provide the earliest observable signs of health impairment, discernable prior to clinical manifestation [14][15][16]. The utility of the methodology used in our study relies on the assumption that oil-induced pathology in sea otters is accompanied by predictable and specific changes in gene transcription.In 2008, we sampled sea otters in previously oiled and unoiled areas of WPWS and compared these to samples from reference (i.e., deemed clinically normal) sea otters from the Alaska Peninsula and captive, healthy sea otters from aquaria [6]. We concluded that sea otters in oiled areas had gene transcription patterns consistent with chronic, low-grade exposure to organic compounds. In 2010 and 2012, we resampled sea otters in the same areas of WPWS to evaluate whether gene transcription patterns observed in 2008 persisted. To provide a broader geographic and temporal interpretation for the analysis of WPWS samples collected in