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Screening for a 27-bp deletion in the band 3 protein gene that causes Southeast Asian/Melanesian ovalocytosis (SAO) was carried out using the PCR method among 15 Southeast Asian populations of Thailand (Akha, Hmong, Isaan, Red Karen, White Karen, Black Lahu, Lisu, Manni, Shan, and central Thais) and Indonesia (Bugis, Dayak, Javanese, Madurian, and Toraja). Individuals with the 27-bp deletion were identified only in the Bugis of southern Sulawesi, the Dayak of southern Borneo, and Javanese of central Java. The gene frequency of the 27-bp deletion in the general population was rather low: 0.012 and 0.013 in the Dayak and the Bugis, respectively. This restricted ethnic and geographic distribution of the 27-bp deletion suggests (1) local differentiation in the prevalence of this deletion in a given ethnic group and (2) the presence of molecular heterogeneity of SAO.