Aschersonia placenta had been recognized as an important fungal pathogen of whiteflies. In recent years, natural occurrence of Aschersonia in whitefly populations was observed in many citrus orchards in the southern regions of China. We analyzed 60 A. placenta isolates obtained from Chinese citrus orchards, using inter-simple sequence repeats to examine the genetic diversity and to determine whether intraspecific variation is correlated with geographic origin. One hundred and fourteen fragments were generated from these isolates; 97% were polymorphic. The Nei's gene diversity (H) was estimated to be 0.1748 within the populations (range 0.0974-0.2179) and 0.3057 at the species level. Analysis of molecular variance showed that the genetic variation was found mainly within populations (74.9%). The coefficient of gene differentiation (GST = 0.4315) indicated that 56.85% of the genetic diversity resided within populations. The Mantel test revealed no significant correlation between the genetic distance and the corresponding geographical distance (r = 0.142 and P = 0.887); the unweighted pair-group method using arithmetic average clustering gave similar results.