Arctic Grayling Thymallus arcticus were historically found throughout the northern half of Michigan’s Lower Peninsula but were extirpated from the state by 1936. By addressing issues from previous reintroduction efforts and employing instream rearing (Remote Site Incubator) approach to stocking, numerous partners are working to reintroduce Arctic Grayling to Michigan with hopes of reestablishing self-sustaining populations. With over 47,000 km of coldwater stream habitat in the state and limited numbers of eggs for reintroductions, a prioritization framework was needed to provide a standardized, fine-scale method for rating suitability of streams for reintroductions. Through facilitated discussions with stakeholders and experts, we developed an overall prioritization framework for rating Michigan streams with components evaluating a reach’s thermal, instream habitat, biological, and connectivity characteristics. Within the context of this broader framework, we developed the habitat rating component for assessing suitability of instream conditions for egg, fry, juvenile, and adult life stages of Arctic Grayling. Life-stage specific habitat metrics and scoring criteria from this effort were used to rate habitat conditions for 45 reaches in tributaries of Michigan’s Manistee River, enabling identification of reaches likely having instream habitat most suitable for Arctic Grayling. Numbers of reaches meeting or exceeding 60%, 70%, and 80% of the maximum score for overall habitat suitability were 31, 8, and 1. Upon completion of the fish assemblage and connectivity components, the prioritization framework and habitat rating process described here will be used for comparing suitability among streams throughout the historic range of Arctic Grayling in Michigan and guiding reintroduction efforts. Though it will take considerable time before instream habitat suitability criteria can be evaluated for all life stages of Arctic Grayling in Michigan, the collaborative stream prioritization framework developed for Arctic Grayling reintroduction can be readily adapted to reintroduction efforts for other species elsewhere.