Background: Plasmodium falciparum's biodiversity still seems to be argumentative, and hinders malaria control, the current study aimed to characterize P. falciparum isolates for genetic markers polymorphism of (msp-1(k1 and ro33) and (msp-2 (FC27 and 3D7)) among malaria-infected Sudanese children. Methods: A total of 100 blood samples from patients were collected from April to August 2019. Blood films and PCR confirmed P. falciparum mono-infections and following gel electrophoresis of DNA products from nested polymerase chain reactions (PCR) targeting msp-1 diversity (K1 and ro33) and merozoite surface protein 2 (msp-2 (FC27 and 3D7)), the analysis of genetic diversity of P. falciparum was carried out by length polymorphism. Data were collected using a structured questionnaire. Results: Among 100 patients were enrolled there were 43% in age group 5 – 10 years and the majority of children were female (65%), the mean of parasite density was (57.320 parasites/ml). The analysis revealed strong allelic diversity, as distinct allelic from 23 and 18 were respectively detected in msp 1 and msp 2 in participants with complicated malaria attack, while only 14, 12 allelic from in msp 1 and msp 2 in participants with uncomplicated malaria attack. At each locus, family distribution in patients with uncomplicated malaria was significantly 17%, and 40% for K1, and RO33 of msp-1 respectively (P. value, 0.03/CI= 2.700). Conclusion: The study concludes that there is high genetic diversity and allelic distribution revealed among the Sudanese population. Even though the used approach had limits, this research demonstrates high polymorphisms in Khartoum state with 23 and18 different alleles of MSP 1 and MSP 2 respectively. The frequency of K1allele in MSP1 of plasmodium falciparum in malaria patients is significantly more predominant than the frequency of the RO33 allele in malaria patients samples, and it correlates with server malaria.