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<i>Holospora</i>-like bacteria (HLB) are obligate intracellular <i>Alphaproteobacteria</i>, inhabiting nuclei of <i>Paramecium</i> and other ciliates such as “<i>Candidatus</i> Hafkinia” is in <i>Frontonia</i>. The HLB clade is comprised of four genera, <i>Holospora</i>, <i>Preeria</i>, “<i>Candidatus</i> Gortzia”, and “<i>Candidatus</i> Hafkinia”. These bacteria have a peculiar life cycle with two morphological forms and some degree of specificity to the host species and the type of nucleus they inhabit. Here we describe a novel species of HLB—“<i>Candidatus</i> Gortzia yakutica” sp. nov.—a symbiont from the macronucleus of <i>Paramecium putrinum</i>, the first described HLB for this <i>Paramecium</i> species. The new endosymbiont shows morphological similarities with other HLB. The phylogenetic analysis of the SSU rRNA gene places it into the “<i>Candidatus</i> Gortzia” clade.