Permafrost considerably influences boreal forest ecosystems by constraining the niche space of woody plants. The permafrost influence on the ecosystems could dramatically change with permafrost thawing owing to recent rapid climate warming. However, it remains unclear how shrub species dominating the understory in boreal forests are associated with the permafrost environments. We investigated two closely related common shrubs, Labrador teas (Ericaceae,Rhododendron subsect. Ledum): R. groenlandicum and R. tomentosum, which exist sympatrically in the discontinuous permafrost zone of the Interior Alaska. We employed field surveys and trait measurements across permafrost gradients under the same climatic conditions to examine the associations among permafrost environments, populations, and leaf traits of the two species. Contrastive habitats were found between the two species: R. groenlandicum is abundant under darker, drier, thicker-active-layer conditions, whereas R. tomentosum is common under brighter, wetter, thinner-active-layer conditions. This suggests that habitat segregation between these species occurs in the discontinuous permafrost zone. Rhododendron tomentosum dominating permafrost conditions had more conservative leaves compared to R. groenlandicum. Moreover, both species had more conservative leaves under permafrost conditions. These intraspecific variations were mainly directly associated with canopy openness in R. groenlandicumbut with active-layer thickness in R. tomentosum. In summary, our study suggests that large environmental variations driven by the inhomogeneous permafrost distributions can lead to the sympatric distributions of closely related shrub species in the discontinuous permafrost zone, and that the conservative leaves can contribute to their adaptation under permafrost conditions.