Predator-prey interactions are often highly co-evolved, with selection over time for prey with morphological and behavioral traits that minimize predation risk. Consequently, in many environments prey choose among potential habitats according to their refuge value. It is unclear, however, when presented with new habitats, if prey are able to evaluate the predation risk of these relative to familiar habitats and utilize these in accordance with their value. We tested whether, along the east coast of the USA, native mud crabs Panopeus herbstii utilize the non-native alga Gracilaria vermiculophylla according to its relative refuge value. Experiments examining predation by blue crabs Callinectes sapidus on mud crabs revealed that the non-native alga had an intermediate refuge value relative to native oysters, which were the most protective, and unvegetated sediment, which was the least. In subsequent choice experiments, mud crabs selected oysters over alga over unvegetated sediment, in accordance with habitat refuge values. Further, in field experiments, the use of Gracilaria by mud crabs was inversely related to the proximity of the alga to the preferred habitat type, oysters, and was reduced by the presence of a blue crab predator. Consequently, mud crabs are utilizing the non-native alga Gracilaria in accordance with its intermediate refuge value. The relative refuge value of non-native vs native habitat-forming species may provide a baseline expectation against which to measure the speed of learning and opportunism in the response of native prey to novel protective habitats.