Objective To investigate the incidence, clinical patterns, and species distribution of pathogenic fungi of onychomyeosis in patients with chronic viral hepatitis (CVH), and to analyze the relationship between onychomycosis and CVH. Methods From November 2005 to October 2006, direct microscopy and fungal culture were performed on nail samples from CVH patients with clinically suspected onychomycosis in the two largest institutions for communicable disease control in Guangzhou city. The incidence, clinical patterns, and species distribution of pathogenic fungi of onychomycosis were assessed based on the findings in mycologic examinations. Results The study randomly recruited 995 patients with CVH, and onychomycosis was diagnosed in 116 patients. The incidence of onychomycosis was 11.66% in total, 6.20%, 8.59%, 14.09%, 19.67% in patients with mild, moderate, severe and extremely severe CVH respectively, 7.09%, 17.29%, 19.13% and 27.27% in patients with a clinical course of CVH of 0.5-9 years, 10-19 years, 20-29 years, ≥30 years respectively. The most common clinical pattern was distal and lateral subungual onychomycosis (DLSO, 69.83%), followed by total dystrophic onychomycosis (TDO, 14.66%). Among the pathogenic fungi, dermatophytes amounted to 71.43%, yeasts 21.43%, moulds 7.14%, and Trichophyton rubrum was the most frequently isolated fungus (42.86%). Conclusions The incidence of onychomycosis in patients with CVH is correlated with the severity and course of CVH. Among these patients, the most common clinical pattern is DLSO with the most frequent fungal species being dermatophytes and predominant fungal isolate being Trichophyton rubrum.