Chromobacterium haemolyticum is a fatal gram-negative bacterium, which had been found that has the ability to infect human. In this study, we detected a nonpigmented, β-hemolytic gram-negative bacillus from fecal samples of piglets with severe diarrhea and death. Analysis of the 16S rRNA gene sequence indicated it was most closely related to Chromobacterium haemolyticum, however only with 79% identities, indicating that this bacterium may be a new type of Chromobacterium haemolyticum. Diarrhea was reproduced in experimental pigs with one of the isolates strains, designated GDHYZ30 strain. Intramuscular injection of the GDHYZ30 strain can cause death of the piglets, and irrigated challenge induced piglets diarrhea. To further elucidate the mechanism of pathogensis of this bacterium, whole genome sequencing was used to analyze and annotate the GDHYZ30 strain. The full-length genome of the strain was 4785117bp, the G+C content was 62.67%, and it encoded 4398 genes, in which 57 drug resistance genes, and 390 virulence factors were included. It is worth noting that this novel Chromobacterium haemolyticum has been isolated from several other pig farm water samples and pig feces samples with unexplained diarrhea. To our knowledge this is the first report that a novel Chromobacterium haemolyticum as a new pathogen causing diarrhea and death in piglets and transmiting through water sources. And the genetic characteristics of the bacteria are analyzed by whole gene sequencing, which provides a reference for the prevention of human and animal infections and food safety.