Infectious keratitis after penetrating keratoplasty (PK) is a devastating condition that may result in graft failure and poor visual outcome. In this study, we retrospectively reviewed the medical records of patients who underwent PK between 2009 and 2014, and recorded those who developed infectious keratitis. We compared the predisposing factors and organisms isolated to those identified in our previous study, conducted between 1989 and 1994. The incidence of post-PK infectious keratitis decreased from 11.6% (41 out of 354 cases, 1989-1994) to 6.5% (9 out of 138 cases, 2009-2014). Graft epithelial defect and suture-related problems remained the leading two risk factors of infectious keratitis after PK. Gram-positive and Gram-negative bacterial infection decreased from 58.5% and 46.3% to 11.1% and 22.2%, respectively (P = 0.023 and P = 0.271). In contrast, fungus infection increased from 9.8% to 66.7% (P = 0.001); fungi have become the major pathogen for post-PK infectious keratitis. In conclusion, while the incidence of post-PK infectious keratitis has decreased over time, the number and frequency of fungal infections have significantly increased in the recent study period. Clinicians should be aware of the shifting trend in pathogens involved in post-PK infectious keratitis.