| Summary: | This study aimed to molecularly survey and evaluate the genetic diversity of <i>Bartonella</i> spp. in mongooses and their fleas from St. Kitts. Spleen (<i>n</i> = 54), blood (<i>n</i> = 71), and pooled flea samples, all identified as <i>Ctenocephalides felis</i> (<i>n =</i> 53), were submitted to TaqMan real-time quantitative PCR (qPCR) targeting <i>Bartonella</i>-<i>nuoG</i> fragment (84 bp). Positive samples underwent further conventional PCR assays targeting five loci (<i>gltA</i>, <i>rpoB</i>, <i>fstZ</i>, <i>nuoG</i>, and ITS), subsequent sequencing, and phylogenetic and haplotype analyses. The overall occurrence of <i>Bartonella</i> spp. in mongooses and fleas was 51.2% (64/125 [95% CI (42.1–60.2%)]) and 62.3% (33/53) [95% CI (47.9–75.2%)]), respectively. From samples sequenced across the five loci, 50.8% (33/65) were identified as <i>Bartonella henselae</i>, 26.2% (17/65) were 96.74–99.01% similar by BLAST analysis to an unidentified <i>Bartonella</i> sp. previously reported in Japanese badgers (<i>Meles anakuma),</i> and 23.1% (15/65) were co-infected with both species. Nucleotide polymorphism analysis showed low diversity amongst haplotypes but did concur with phylogenetic analysis, placing the unidentified species in a separate clade from <i>B. henselae</i> by multiple mutational events. Our data confirms that mongooses and <i>Ctenocephalides felis</i> fleas collected from them are not only potential reservoirs for <i>B. henselae</i> but also a novel <i>Bartonella</i> sp. which we propose be called ‘<i>Candidatus</i> Bartonella kittensis’.
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