The present paper is a report on the prevalence of Haemoglobin E among four endogamous populations of Manipur (India) named the Kabui, Koireng, Simte and the Meitei. The average frequency of allele HbbE observed among the Meitei is 0.101. However, the frequency of HbbE ranges from 0.045 to 0.226 among various sections of the Meitei. The frequency of HbbE among the Phayeng Chakpa shows the highest value (0.226) while the Ningthoukhong Meitei shows the lowest (0.045). The frequency of HbbE among the hill Kabui population is 0.035 followed by the Koireng (0.029) and the Simte (0.012). The frequency of HbbE among the various tribal populations of malaria endemic zones of Manipur is below 0.04. It is indicative that the ethnic origin and marriage system may be the responsible factors for variation in the frequencies of HbE gene among the populations of Manipur. In the present study, neither protective advantage of HbbE against malaria nor harmful effect of homozygous (HbEE) genotype could be satisfactorily established.