Genetic typing of the parasites has been used as a marker for determining the level ofrntransmission, level of acquired immune response and for analyzing the relationshiprnbetween infection and pathogenesis of malaria. The present study is aimed at describingrnthe prevalent parasite population dynamics of Ethiopian isolates in relation to age relatedrnprotection and parasite pathogencity in different geographical settings. For this purpose,rnfinger prick blood samples were collected on filter paper and slides from microscopicallyrnconfirmed malaria patients (age > 3 months) attending health clinics in Arbaminch, Burie,rnDerra, and Zeway. Then DNA was extracted by chelex extraction method and used forrnPCR amplification: family-specific nested PCR of MSP-2 gene for genotyping P.rnfalciparum and PCR-RFLP analysis of MSP-3Î± gene was used to genotype P.vivax. Thernfindings of the study showed that mean number of genotypes for P. falciparum was 2.34rnwith a range of 1 to 6 and 78.2% of the isolates were multiclonal majority of themrncarrying double infection. Thirty-seven alleles were detected in FC27 (17) and IC-1 (20)rnallelic families. No significant associations found between age and multiplicity ofrninfection while the difference was significant in different geographical areas. Fifteenrndifferent genotypes of P. vivax were found and 7.2% of the isolates were multiclonal.rnBased on the results of the study it was concluded that Ethiopian isolates P. vivax and P.rnfalciparum are highly diverse with a pattern similar to other countries with the same levelrnof transmission. Further nation wide investigation is recommended to better understandrnpolymorphism of malaria parasites in relation to acquired immune response andrnpathogenicity.