<i>Corynebacterium diphtheriae</i> is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic <i>C. diphtheriae</i> infections. Here, a <i>C. diphtheriae</i> strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of <i>C. diphtheriae</i> revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the <i>C. diphtheriae</i> NCTC 11397 ^T reference genome than all other <i>C. diphtheriae</i> genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new <i>C. diphtheriae</i> subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: <i>C. diphtheriae</i> subsp. <i>lausannense</i> subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and <i>C. diphtheriae</i> subsp. <i>diphtheriae</i> subsp. nov, regrouping all other <i>C. diphtheriae</i> in the dataset (instead of lineage-1). Interestingly, members of subspecies <i>lausannense</i> displayed a larger genome size than subspecies <i>diphtheriae</i> and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks <i>csn2</i> or <i>cas4</i> , which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.