Malaria is an infectious disease caused by Plasmodium sp. This disease has a high prevalence in Indonesia, especially in Jayapura. This is due to the high polymorphism in the Plasmodium genome especially in areas that encode surface proteins. Therefore, in this study, we analyzed the allele polymorphism as well as detected the MSP1 epitope antigen  candidate on block 2 P. falciparum. Clinical samples of selected malaria patients followed the consecutive sampling method, examining malaria parasites with blood preparations on glass objects observed through a microscope. Plasmodium DNA was isolated from the blood of malarial positive patients. The block 2 MSP1 gene was amplified using PCR method and cloned using pGEM-T easy vector then transformed to TOP'10 E.coli. Positive colonies selection was performed with blue white screening. DNA sequence analysis was done through alignment and formation of phylogenetic tree using MEGA 6 software and IEDB software to predict epitope candidate for P. falciparum. PCR amplification results show the target gene size about ± 1049 bp. The results of MSP1 nucleotide alignment analysis reveal that block 2 MSP1 genes derived from the sample of malarial patients were distributed in four different allele family groups, K1 (7), MAD20 (1), RO33 (0) and MSP1_Jayapura (10) alleles. Symptomatic signs have a significant difference as a trigger of detectable allele variation (U <0.05). In this research, in silico study shows that there is a new epitope antigen candidate from the MSP1_Jayapura allele and it is predicted to be recognized by B cells with 17 amino acid lengths in the amino acid sequence 187 to 203. MSP1 can be promoted to be a specific antigen and predicted epitope which will be used for the development of diagnostic and malaria vaccine therapy.