| Summary: | We sequenced the complete mitogenomes, 18S and 28S rRNA of two new <i>Scarites</i> isolates, collected in Eastern Nebraska and Northern Arkansas (US). Based on molecular sequence data comparison and morphological characteristics, the new isolates were identified as a subspecies of <i>Scarites subterraneus</i> Fabricius 1775, for which we propose the subspecies names ‘<i>nebraskensis</i>’ and ‘<i>arkansensis</i>’. The new 18S and 28S rRNA sequences were found to be 99% and 98% identical to <i>Scarites subterraneus</i>. There are no other <i>Scarites</i> 18S or 28S rRNA sequences in the Genbank database, however, phylogenetic analysis of the Cox1 genes showed <i>S. vicinus</i> Chaudoir, 1843, and <i>S. aterrimus</i> Morawitz, 1863, as the closest relatives. This is the first report of a mitogenome for <i>S. subterraneus</i>, and only the second mitogenome for that genus. The nucleotide sequence identity between the mitogenomes of the two isolates is 98.8%, while the earlier sequenced <i>S. buparius</i> Forster 1771 mitogenome is more distantly related, with only 90% (to ssp. <i>nebraskensis</i>) and 89% (to ssp. <i>arkansensis</i>) overall nucleotide sequence identity. These new mitogenomes, and their phylogenetic analysis, firmly establish the position of <i>Scarites</i> on the Carabidae family tree and further refine the genus. In addition to the molecular data provided for the <i>Scarites</i> species, this approach also allowed us to identify bacterial and viral signatures for <i>Providencia</i>, <i>Myroides</i>, <i>Spiroplasma</i>, and a giant <i>Nucleocytoviricota</i> virus, associated with the <i>Scarites</i> species. We hereby present a simple and efficient protocol for identification and phylogenetic analysis of <i>Scarites</i>, that is applicable to other Coleoptera, based on total DNA extraction and Illumina short-read Next-Gen sequencing.
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