The genus Shewanella is rapidly expanding, with new species being discovered frequently. Four species have been identified as pathogenic to humans, with Shewanella algae being most relevant. Evaluation of the clinical significance of Shewanella spp. still suffers from the imprecision of species identification. In addition, the origin of S. algae strains causing disease is unclear. To shed light upon these questions we re-identified reported S. algae isolates on the species level based on the analysis of the partial sequences of the 16S rRNA and gyrB genes in combination with multilocus sequence typing that included six housekeeping loci. The analysis of a collection of 23 S. algae isolates of clinical and environmental origin, the publicly available genome sequences of six additional S. algae strains and type strains of closely-related species showed the existence of a remarkable haplotypic diversity within the S. algae clade. Three of the analyzed strains are suggested to be assigned to a species different from S. algae. A clinical isolate was thus reclassified as S. chilikensis, thereby constituting the first known case of human infection by this species. Our study emphasizes the application of high resolution molecular markers for species identification. The taxonomic resolution of the S. algae clade is still unclear.