Identifying habitat preferences of species of concern is fundamental to the practice of conservation, but disturbances and other environmental processes can substantially affect suitability. Trifolium stoloniferum, or running buffalo clover, is a federally endangered plant species that occurs on the Fernow Experimental Forest in West Virginia. Previous work and extensive anecdotal evidence suggests that this species is maintained in part by periodic disturbances to its habitat. In the Fernow Experimental Forest, this disturbance is in the form of intermittent logging activities. We investigated the role of forest harvesting practices and environmental variables in fostering T. stoloniferum at the stand level. Censuses have been conducted on T. stoloniferum occurrences in the Fernow since 1994, and occurrences are grouped by subcompartment or watershed, which are the basic management units within this experimental forest. Site characteristics and disturbance history were assessed for their impact upon T. stoloniferum presence and density. Classification tree analysis identified total number of forest harvest events in a subcompartment since 1948 as the most important predictor of T. stoloniferum presence or absence. Regression tree analysis identified aspect as important in determining T. stoloniferum abundance, with west-facing compartments supporting larger populations. This study confirms the importance of disturbance in maintaining T. stoloniferum populations. However, site characteristics independent of disturbance history are also predictors of T. stoloniferum presence and abundance, suggesting that managers attempting to restore or create habitat for T. stoloniferum should account for the interaction between disturbance history and site characters in determining suitability of habitat for T. stoloniferum.