Whitebark pine (Pinus albicaulis Engelm.) is a key component of subalpine and alpine ecosystems in the northern Cascades. The species’ survival is threatened by white pine blister rust, mountain pine beetle, fire exclusion, and climate change. We monitored whitebark pine in permanent plots in two national parks three times between 2004 and 2016. The proportion of live trees showing evidence of blister rust infection increased in North Cascades National Park Service Complex from 32% in 2004 to 51% in 2016 and from 18% to 38% in Mount Rainier National Park. Mortality increased from 7% to 21% in North Cascades National Park Service Complex and 38% to 44% in Mount Rainier National Park. The percent of live infected and dead whitebark pine increased with south and east aspects and mortality decreased with elevation. Annualized mortality rates calculated for the entire study period were 1.5% in Mount Rainier National Park and 2.3% in North Cascades National Park Service Complex. Although these rates decreased between the first time period (2004–2009) and the second time period (2009–2016), the prevalence of infected and dead whitebark pine increased across all park landscapes over time and increased in smaller diameter whitebark pine trees.