In this study, we sequenced the genome of P. pnomenusa RB38 and reported the finding of a pair of cognate luxI/R homologs which we firstly coined as ppnI, which is found adjacent to a luxR homolog, ppnR. An additional orphan luxR homolog, ppnR2 was also discovered. Multiple sequence alignment revealed that PpnI is a distinct cluster of AHL synthase compared to those of its nearest phylogenetic neighbor, Burkholderia spp. When expressed heterologously and analysed using high resolution tandem mass spectrometry, PpnI directs the synthesis of N-octanoylhomoserine lactone (C8-HSL). To our knowledge, this is the first documentation of the luxI/R homologs of the genus of Pandoraea.