Three genera in the Rubiaceae (
Pavetta
,
Psychotria
and
Sericanthe
) harbour bacterial endosymbionts within leaf nodules or galls. The present paper identifies the bacterial endophytes in three leaf-nodulating
Pavetta
species. In order to reveal their identity and assess their phylogenetic position, 16S rRNA,
recA
and
gyrB
genes were sequenced from an extensive sampling of
Burkholderia
strains. This multigene approach results in a robust phylogeny, which places the bacterial endosymbionts of
Pavetta
at two distinct positions within the genus
Burkholderia
(class
Betaproteobacteria
), suggesting that leaf-nodulating endosymbionts within
Pavetta
have different origins. The endophytes of nodulated
Psychotria
species were recognized as the closest relatives to the
Pavetta
endosymbionts. Our results suggest that the endosymbionts of
Pavetta
represent novel species, which can be classified as ‘
Candidatus
Burkholderia hispidae’, ‘
Candidatus
Burkholderia rigidae’ and ‘
Candidatus
Burkholderia schumannianae’.