Strategies to mitigate climate change can protect different types of cool environments. Two are receiving much attention: protection of ephemeral refuges (i.e., places with low maximum temperatures) and of stable refugia (i.e., places that are cool, have a stable environment, and are isolated). Problematically, they are often treated as equivalents. Careful delineation of their qualities is needed to prevent misdirected conservation initiatives; yet, no one has determined whether protecting one protects the other. We mapped both types of cool environments across a large (∼3.4M ha) mixed-use landscape with a geographic information system and conducted a patch analysis to compare their spatial distributions; examine relations between land use and their size and shape; and assess their current protection status. With a modest, but arbitrary, threshold for demarcating both types of cool environments (i.e., values below the 0.025 quantile) there were 146,523 ha of ephemeral refuge (62,208 ha) and stable refugia (62,319 ha). Ephemeral refuges were generally aggregated at high elevation, and more refuge area occurred in protected areas (55,184 ha) than in unprotected areas (7,024 ha). In contrast, stable refugia were scattered across the landscape, and more stable-refugium area occurred on unprotected (40,135 ha) than on protected land (22,184 ha). Although sensitivity analysis showed that varying the thresholds that define cool environments affected outcomes, it also exposed the challenge of choosing a threshold for strategies to address climate change; there is no single value that is appropriate for all of biodiversity. The degree of overlap between ephemeral refuges and stable refugia revealed that targeting only the former for protection on currently unprotected land would capture ∼17% of stable refugia. Targeting only stable refugia would capture ∼54% of ephemeral refuges. Thus, targeting one type of cool environment did not fully protect the other.