Phytophthora pinifolia is the causal agent of the recently discovered needle disease of Pinus radiata in Chile, referred to as “Daño Foliar del Pino” (DFP). The genetic structure of the pathogen population is unknown, which hinders our understanding of its appearance and spread in Chile since 2004. In this study, a population of 88 cultures of P. pinifolia isolated from P. radiata at several localities in Chile was evaluated for genotypic diversity using amplified fragment length polymorphisms (AFLPs). Results of the AFLP analyses showed that the P. pinifolia population in Chile consists of two near identical genotypes but with no genetic differentiation based on geography, year of isolation or the part of the tree from which the isolates were obtained. Mating experiments did not lead to the production of gametangia suggesting that the organism is sterile. The fact that a single clonal genotype dominates the population of P. pinifolia in Chile supports the hypothesis that P. pinifolia was recently introduced into this country and that its impact is due to a new and susceptible host encounter.