Polar bears are a sea ice-dependent carnivore, sensitive to sea ice habitat loss. Climate change has negatively affected sea ice habitat through much of this species' range. We applied landscape fragmentation analysis to quantify polar bear sea ice habitat loss and fragmentation trends (1979–2008) in Foxe Basin, Hudson Strait and Hudson Bay, Canada. Microwave satellite derived monthly mean sea ice concentration maps were classified into four habitat quality categories, and the trends in fragmentation metrics were analyzed. In all regions where preferred habitat declined, sea ice season length decreased and habitat fragmentation increased. The observed trends may affect polar bear movement patterns, energetics and ultimately population trends. Monitoring of sea ice habitat condition in combination with harvest data can provide a dynamic approach to population management and conservation.