Background This study was to review the distribution and shifting trend of fungal of culture specimens isolated from eyes of patients at the Beijing Institute of Ophthalmology, Tongren Hospital, Beijing, China. Methods The fungal culture-positive rate, the distribution and change of isolates of 2609 specimens collected in a 12-year period (1989-2000) were retrospectively analyzed. Results In 775 positive cultures, 707 specimens (91.2%) were from the cornea, 22 (2.8%) from the conjunctiva, 15 (1.9%) from the anterior chamber, 9 (1.2%) from the vitreous body, 3 (0.4%) from the lacrimal sac, and 19 (2.5%) from other parts of the eye. The average culture-positive rate was 29.7%. The ratio of the positive cultures in the first half year (from January to June) to those in the second half (from July to December) was 1 : 2. 1. The main genus cultured was Fusarium sp (58.7%), followed by Aspergirum sp (16.8%). The percentage of Fusarium sp was increased from 53.6% (1989 - 1994) to 60.2% (1995 - 2000), whereas the percentage of Aspergirum sp was decreased from 22.3% (1989 - 1994) to 15.1% (1995 - 2000). Conclusions Fusaruim sp is one of the most predominant pathogens of ocular fungal infection in northern China and its incidence tends to increase, but that of Aspergirum sp to decrease. It is very important to recognize the distribution and shifting trend of pathogenic fungi in the diagnosis, prevention and treatment of fungal keratitis.