Background: Historical and anthropological data suggest the presence of descendents of Changos, Cuncos, Chonos and Yamanas, South American indian populations, in certain Chilean coastal villages. Aim: To assess the degree of South American indian admixture in Chilean coastal villages using protein markers, to complete the assessment of human biological diversity of Chile. Subjects and methods: AB0, Rh, MNS, Duffy and Kidd blood group systems were assessed in 47, 48, 55 and 24 individuals from Paposo, Carelmapu, Laitec and Ukika respectively. Phenotypic and gene frequencies were calculated. The degree of South American indian admixture was estimated from the AB0*0 allele and Rh*dce haplotypes. Results: High frequencies of AB0*0, Fy*a, Jk*b alleles, Dce and Ms haplotypes were found in all villages, consistent with the pattern expected for South American Aboriginal populations. The highest presence of South American indian admixture was present in Laitec with 80% and in Ukika with 74%. The figures for Paposo and Carelmapu were 60 and 65% respectively. Conclusions: According to South American indian admixture estimates, the genetic isolation of coastal populations is lower than that of inland subjects, suggesting that sea proximity facilitates gene flow.