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Malaria is an infectious disease caused by plasmodium that lives and breeds in the red blood cells, transmitted by the Anopheles mosquito. During this time, the paramedics to diagnose symptoms use any imagery that is done manually. In the identification analysis of the malaria parasite cell infection, there is a possibility of human error factor done by paramedics because of the number of samples analyzed. This case is because the human eye tends to be tired while working continuously, leading to misclassification and treatment that is not right. Therefore, it takes a computer-based system that facilitates image processing to paramedics or laboratory technicians to identify the parasite cells and reduce human error instances. This research conducted on identification of the thresholding and watershed of segmentation method for three types of plasmodium parasite, namely Plasmodium falciparum, Plasmodium malaria, and Plasmodium vivax. This study offered modifications thresholding and watershed algorithm. The results showed the success of the technique that can effectively segment on the three types of Plasmodium malaria, which has an accuracy rate above 90% as well as the results of the computation time between the thresholding method could segment imagery for 1-2 seconds and the watershed method intelligent segmented representation for 3-4 seconds.