The phylogeny of ‘Candidatus Phlomobacter fragariae’(Ca. P. fragariae), the agent of the strawberry marginal chlorosis (SMC), and the proteobacterium associated with the low sugar content syndrome of sugar beet (SBRp) is not well understood. The spoT-spoU-recG genetic locus initially characterised by genome walking from a ‘Ca. P. fragariae’ partial spoT sequence was used to determine relatedness of ‘Ca. P. fragariae’ and SBRp with bacteria detected in hemipteran insects. Both plant pathogenic bacteria belong to the same phylogenetic group as bacteria of the arsenophonus clade detected in hemipteran insects. The SBRp is closely related to arsenophonus-like proteobacteria from cixiids and more distantly related to psyllid and delphacid secondary endosymbionts, whereas the relatives of ‘Ca. P. fragariae’ remain to be discovered. No genetic variability was found among isolates of ‘Ca. P. fragariae’ or SBRp. Implications for explaining the emergence of both ‘Ca. P. fragariae’ and SBRp as epidemic plant pathogens are discussed.