We compared habitat use and niche overlap in the closely related seabirds Kittlitz’s (Brachyramphus brevirostris) and Marbled (B. marmoratus) Murrelets in nearshore waters of Prince William Sound, Alaska, in 1996–1998, and examined the relationship between near shore habitat use and morphology of those two species. Within bays, the distribution of Kittlitz’s Murrelet groups diverged the most from randomness for the variables habitat type (preferring [i.e. using significantly more than what is available] glacial-affected and glacial-stream-affected habitats), distance to shore (preferring areas 51–100 m from shore), and water clarity (preferring highly turbid water), whereas the distribution of Marbled Murrelet groups diverged the most from randomness for the variables habitat type (preferring glacial-unaffected habitats), ice cover (preferring areas of no ice), and sea-surface temperature (SST) (preferring temperatures = 6°C). The probability of a group of birds being Kittlitz’s Murrelets was determined most strongly by water clarity. Kittlitz’s Murrelet groups were more common in the more heavily glaciated College and Harriman fjords than in the other two bays and more common in early and midsummer than in late summer; the reverse was true for Marbled Murrelet groups. Marbled Murrelet groups had the least niche overlap with Kittlitz’s Murrelet groups in water clarity, SST, and site, whereas Kittlitz’s Murrelets had the least overlap with Marbled Murrelets in habitat type and water clarity. Similarly, Kittlitz’s Murrelet groups occurred in water significantly more turbid than did Marbled Murrelet groups in two of four habitat types. Kittlitz’s Murrelets had eyes (as indicated by orbit diameter) that were significantly larger in proportional size than Marbled Murrelets. We propose that these two species are specialized for foraging in different water types, with specialization of the Kittlitz’s Murrelet for turbid water of glacial origin leading to optical specialization.