SummaryWe isolated Acanthamoebae from the first two keratitis patients identified in Thailand in 1988 and 1990. The patients developed decreased vision, severe photophobia, severe eye pain and foreign body sensation after minor corneal trauma. The lesions included generalized superficial punctate keratitis, stromal corneal ulcer with keratic precipitate and uveitis in one case, and corneal ulcer with abscess in the other. Both cases were diagnosed by isolation of characteristic trophozoites and cysts of Acanthamoeba from corneal tissue by nonnutrient agar culture method. Based on cyst morphology, A. castellanii and A. polyphaga were detected in one case, and A. castellanii and A. triangularis in the other. Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA-RFLP) revealed that each patient harboured a single parasite population. One shared mtDNA-RFLP with an authentic strain of A. castellanii, and the other gave a new unique pattern. Thus species identification of Acanthamoeba based on cyst morphology per se can be arbitrary, and mtDNA-RFLP may be more appropriate for accurate species/strain differentiation amongst morphologically heterogeneous populations of Acanthamoebae.