Ectoparasitic infestations including pediculosis capitis are common in people of disadvantaged communities as they live in overcrowded institutions, a condition that often favourable for disease transmission. In this study, we evaluated the prevalence of head lice infestation among disadvantaged children aged between five to 14 years-old living in five poor conditions located across the Klang Valley, Malaysia. Of total 335 children examined, 14% were positively infected with head lice. Molecular analysis using the universal cytochrome c oxidase subunit I ( COI) barcoding gene on total of 167 head lice collected in this study indicated they are belonging to the A and C clades; confirming the global distribution of clade A and expansion of clade C in Southeast Asia, which is reported for the first time in Malaysia.