Phytophthora infestans populations can differ in composition as a result of host-specialisation on tomato and potato hosts. In Great Britain many amateur gardeners grow outdoor tomatoes but there is little or no commercial tomato production outdoors. This study analysed isolates of P. infestans from British gardens with twelve multiplexed SSR markers that are used to monitor the disease on commercial potato crops. Samples of P. infestans from tomato hosts were collected in three years and from potato in one year from across Great Britain. Seven previously unreported genotypes were detected in garden populations and higher frequencies of unique clonal lineages (28% to 40%) were present compared with populations from British commercial potato crops reported elsewhere. Garden populations had a lower proportion (11% to 48% less) of the most common lineages (13_A2 and 6_A1) which together made up at least 86% of the commercial potato populations during the sampling period. Host species accounted for only 2.6% of molecular variance detected between garden potato- and tomato-hosted samples. No significant difference in clonal lineage composition was found between host species in Great Britain and this could be due to the whole P. infestans population over-wintering on potato. British garden populations on both hosts were much more diverse than those on commercial potato crops; this finding may be influenced by less frequent fungicide use by gardeners and a higher diversity of un-sprayed susceptible potato cultivars enabling metalaxyl-sensitive and less virulent genotypes to survive in gardens.