The characterisation of Phytophthora infestans isolates is a key step in both monitoring population changes and designing control strategies. A collection of 57 isolates (33 from 2003 to 2005 and 24 from 2011 to 2014) of the Spanish population of P. infestans from different potato fields was characterised in this study. Mating types A1 and A2 have been identified for the first time in Spain by using CAPs markers. A total of 23 samples were classified as A1 mating type and 34 as A2 type. All isolates had the Ia mitochondrial haplotype with one exception which was IIa. Three clonal lineages of P. infestans were detected: 2_A1, 3_A2 and 13_A2 (Blue 13), where a sub-clonal variation was observed within this lineage (13_A2_1, 13_A2_2, 13_A2_3, 13_A2_4, 13_A2_15, 13_A2_68 and 13_A2_new). Two isolates denominated as ‘Misc’ could not be ascribed to any of the genotypes characterised. These results highlight the spread of pathogen clones across Europe during this period and the risks related to the presence of both P. infestans mating types are discussed.