Autecological information targeted towards rare and threatened lichen species is severely lacking. This study adopts the rare British lichen Vulpicida pinastri as a case study species and examines its ecological response to emerging threats: climate change and the recurrent loss of its primary habitat (juniper scrub). We used predictive niche modelling to examine the response of V. pinastri to a range of present-day climatic variables. A successful model was projected for a period during the 2050s based on IPCC climate change scenarios (UKCIP02 data), and threat was estimated as the proportional change in bioclimatic space. To estimate the potential range now and during the 2050s, projected bioclimatic space was masked by a habitat map equivalent to (i) the present-day distribution of juniper and (ii) theoretical juniper distribution based on existing rates of decline. Our results point to potential range loss of V. pinastri with climate warming, exacerbated by the recurrent decline in juniper habitat. This predictive modelling approach was complemented by an assessment of local stand-scale effects. At four sites in north-east Scotland we examined the occurrence and abundance of V. pinastri thalli, in response to juniper spatial distribution, and the life-stage and structure of individual shrubs. Vulpicida pinastri appeared to be dispersal limited at small-scales, and was significantly more abundant on old and degenerate juniper shrubs. Our results evidence a close relationship between management for habitat quality and effective lichen conservation. Effective conservation of V. pinastri must ensure cohorts of older and degenerate juniper shrubs are maintained at sites where the species is expected to be most resistant to long-term climate warming, i.e. in the uplands of north-east Scotland.