Abstract Aim Marginal populations are frequently neglected in static views of vegetation types, particularly when defining conservation reserves. The biogeographical and evolutionary importance of a marginal and endangered population of Pinus canariensis is addressed in this study to ascertain the need for conservation action. Diversity loss between adults and offspring and patterns of seed dispersal and recruitment were examined to provide evidence of recent degradation of marginal P. canariensis pinewoods. The scientific basis for the provision of sound conservation policies was investigated by elucidating the factors responsible for significant population structure. Location An isolated low-density pinewood community confined to the Arguineguin ravine, in south Gran Canaria, Canary Islands. Methods Two cohorts, of centenary trees (those older than 100 years) and young recruits, respectively, were found in a detailed inventory of the pine population in the Arguienguin ravine. Chloroplast and nuclear microsatellites were compared to assess the levels of genetic diversity between adults and recruits. Spatial genetic structure and parentage analysis based on highly polymorphic nuclear and chloroplast microsatellites were examined to test limitations in seed dispersal. The underlying environmental factors that led to a clustering effect in the population were tested using point pattern methodologies. Results Centenary trees retain high levels of genetic diversity and effective population size, suggesting a wider extension of the pinewood forests in the past. A significant loss of genetic diversity was detected between adults and recruits. Pinus canariensis dispersal distances were among the longest ever reported for anemochorous species, suggesting that environmental factors account for recruit clustering. Cluster models showed that recruits tend to aggregate in dry streambeds, where soil and water accumulation favours establishment. Main conclusions Boundary populations of P. canariensis are subjected to fragmentation and reduction in effective population size as a result of human impact. Marginal populations were denser in the past and currently require specific conservation efforts. A severe reduction in genetic diversity compromises the future of present populations. Streambeds appear to play a major role in recruit establishment, but data suggest the absence of limitations to seed dispersal.