Background <p>Globally, the disease ecology of reptiles remains understudied, even for threatened and iconic species such as the Galápagos marine iguana (<i>Amblyrhynchus cristatus</i>). Although marine iguanas are parasitized by distinct species of ticks and mites, research on vector-borne diseases for this species is limited.</p> Methods <p>In this study, we detected 16S ribosomal RNA (rRNA) sequences of <i>Candidatus</i> Allocryptoplasma in transcriptomic data from marine iguana blood samples. These 16S rRNA sequences were further characterized through phylogenetic analysis and a haplotype network.</p> Results <p>Our analysis revealed the first molecular evidence for the infection of marine iguanas with <i>Candidatus</i> Allocryptoplasma, a candidate genus in the family Anaplasmataceae with unknown pathogenic potential, likely transmitted by ticks. Phylogenetic analysis of the novel 16S rRNA sequences together with available Anaplasmataceae sequences confirmed their assignment to this candidate genus. A haplotype network analysis indicated that the agent infecting the marine iguana represents a distinct lineage within the known <i>Ca</i>. Allocryptoplasma diversity.</p> Conclusions <p><i>Candidatus</i> Allocryptoplasma had a high prevalence within marine iguanas, infecting individuals across most of the geographical range of this species. To elucidate the transmission dynamics of this bacterium in the Galápagos ecosystem, ectoparasites of the marine iguana and shared vertebrate hosts should be screened for infection with <i>Ca</i>. Allocryptoplasma.</p> Graphical Abstract <p></p>