Objective: To identify genomic variance of C. difficile strains to determine diversity and transmission potential which can guide future directions in clinical care and hospital policy. Study Design: We analyzed epidemiological and genomic data from 35 patients with laboratory confirmed C. difficile infection (CDI) in two three-month periods in 2011 and 2014 at a large urban hospital. Whole genome sequencing was conducted on all isolates; further analysis was conducted for 13 cases of CDI with the highly virulent NAP1 strain. Results: Overall strain diversity within the hospital was analyzed. Stable prevalence among the NAP1 strain indicated an endemic status; no other strain exhibited a specific pattern. Genomic analysis identified at least 4 distinct subgroups in the NAP1 strain specific to the hospital. Conclusion: Genomic analysis is necessary to unequivocally identify C. difficile transmission and can provide both clinical and procedural benefit.