Scotts Creek, in Santa Cruz County, Calif., supports the southernmost extant population of Coho Salmon (Oncorhynchus kisutch) in North America. In 1997, the California Department of Fish and Game (now Fish and Wildlife) conducted an extensive habitat typing survey of mainstem Scotts Creek, describing all habitat units from the top of the estuary to the limit of anadromy approximately 12 km upstream. I repeated this survey in 2013 to (1) assess changes in the quantity and quality of instream habitat, (2) compare the current condition to goals and standards established in the federal Central California Coast (CCC) Coho Salmon Recovery Plan, and (3) identify opportunities for possible future restoration. A comparison of the two surveys revealed an overall increase in mean canopy cover, mean bank vegetation, mean percentage instream cover, pool depth diversity, and percentage riffles since 1997, and decreases in mean residual pool depth, percentage flatwater, and number of primary pools. Overall, the percentage of the total mainstem classified as pool habitat did not change between the two survey periods. Results for individual habitat metrics were more variable when the stream was broken into discrete reaches delineated by major tributary junctions. Although a large woody debris (LWD) survey was not conducted as part of the 1997 survey, contrasting our results with data collected during intervening years indicated that instream LWD has become more abundant, primarily due to increases in hard-wood species (i.e., red alder [Alnus rubra] and California bay [Umbellularia californica]). When compared to habitat goals established in the federal CCC Coho Salmon Recovery Plan, Scotts Creek has adequate canopy cover and percentage pools, but is lacking in percentage riffles, instream cover, key pieces of LWD per100 m, and percentage primary pools.