‘Candidatus Phytoplasma prunorum’ is associated with European stone fruit yellows disease, affecting wild and cultivated species of Prunus at different degrees of susceptibility, so far being mainly restricted to Europe. Here, we report draft genome sequences for ‘Ca. Phytoplasma prunorum’ strains ESFY1 and LNS1, which represent the first available for this species. Strain ESFY1 is the causal agent of the European stone fruit yellows disease of Prunus persica in Germany and LNS1, leptonecrosis disease of Prunus salicina in Italy. Their draft genomes consist of 480,123 and 490,930 bases, assembled into 28 and 16 contigs, respectively, with an average GC content of 21.1% and 20.7%, respectively. Analysis of average nucleotide identity values between genomes further supported the delineation of ‘Ca. Phytoplasma prunorum’ as a species distinct from ‘Ca. Phytoplasma mali’, in agreement with previous phylogenetic data.