Members of the phylum Jakobida (superkingom Excavata) are known for their strikingly bacterial-like mitochondrial genomes (mtDNA). These mtDNAs have as many as 67 protein-coding genes, some of which are organised into operons with nearly canonical alpha-proteobacterial gene order. Jakobid mtDNAs also encode a bacterial-type RNA polymerase, which they use for mtDNA transcription rather than the viral type (T7-like) RNA polymerase used by all other eukaryote mtDNAs. This has led to the suggestion that jakobids are unique among eukaryotes in retaining primitive mtDNAs that trace to the mitochondrial progenitor. However, molecular phylogeny fails to place jakobids as sister to all other eukaryotes. Furthermore, we show that at least one of the uniquely bacterial-like mtDNA genes of the jakobid Andalucia godoyi is not in fact primitive, but rather appears to have been derived relatively recently by horizontal transfer from bacteria. These data suggest an alternative explanation for the bacterial-like nature of jakobid mtDNAs.