The McClelland Lake Wetland Complex is a large (3,481 ha), boreal, wetland complex dominated by peatlands located in northeastern Alberta, Canada. We intensively sampled the bryophyte flora in 44 sites chosen to capture all landscape features of the wetland. We furthermore partitioned these 44 sites into 67, structurally defined stands. One hundred and fourteen species of bryophytes (91 mosses and 23 hepatics) were found. Mean stand species richness is 16.6, with a range of 2–41 species. Thirty-nine species were recorded only 1–2 times in the 67 stands and these are defined as locally rare species. Additionally, 18 species were recorded that are currently on the Alberta Rare Species Tracking List (ANHIC), although commonness of some within the complex suggests regional under-collection. A strong relationship was found between species richness and locally rare species occurrence at both the site and stand levels. Neither species richness nor locally rare species occurrence is related to landscape position within the wetland complex nor to internal wetland chemical gradients. Both species richness and local species rarity are influenced by stand type and structure. Shrubby, wooded, or forested stands contain 70% of the locally rare species occurrences, and swamps and wooded fens are species rich habitats. Stands with high numbers of locally rare species also tend to be stands that have high species richness; however, not all stands with high species richness have high numbers of locally rare bryophytes. Indicators and assessment protocols based on rare species and richness are developed to define Key Habitats for this wetland complex. Criteria for Key Habitats are stands with both high species richness and high numbers of locally rare species—‘Category 6’ stands, and these are identified as significant features in developing management protocols for bryophyte species and wetland function. Six ‘Category 6’ stands capture 58% of the locally rare species and 90% of the total wetland species richness. All six Key Habitats are wooded or forested.