Some well-known Clostridiales species such as <i>Clostridium difficile</i> and <i>C. perfringens</i> are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as <i>Clostridium tertium</i> and <i>C. paraputrificum</i>. Three fecal isolates were identified as <i>Clostridium tertium</i> (Gcol.A2 and Gcol.A43) and <i>C. paraputrificum</i> (Gcol.A11) during public health screening for <i>C. difficile</i> infections in Colombia. <i>C. paraputrificum</i> genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the <i>C. tertium</i> genomes than in the <i>C. paraputrificum</i> genomes. <i>C. difficile tcdA</i> and <i>tcdB</i> toxins encoding homologous sequences and other potential virulence factors were also identified. <i>EndoA</i> interferase, a toxic component of the type II toxin-antitoxin system, was found among the <i>C. tertium</i> genomes. <i>toxA</i> was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the <i>C. tertium</i> genomes compared with the <i>C. paraputrificum</i> genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in <i>C. paraputrificum</i>), with proteins involved in sporulation processes more highly represented in <i>C. tertium</i>. These finding suggest the need to advance in the study of those species with potential importance at public health level.