Malaria is categorised as a dangerous disease that can cause fatal in many countries. Therefore, early detection of malaria is essential to get rapid treat- ment. The malaria detection process is usually carried out with a 100x magnifica- tion of thin blood smear using microscope observation. However, the microbiologist required a long time to identify malaria types before applying any proper treatment to the patient. It also has difficulty to differentiate the species in trophozoite stages because of similar characteristics between species. To over- come these problems, a computer-aided diagnosis system is proposed to classify trophozoite stages of Plasmodium Knowlesi (PK), Plasmodium Falciparum (PF) and Plasmodium Vivax (PV) as early species identification. The process begins with image acquisition, image processing and classification. The image proces- sing involved contrast enhancement using histogram equalisation (HE), segmen- tation procedure using a combination of hue, saturation and value (HSV) color model, Otsu method and range of each red, green and blue (RGB) color selec- tions, and feature extraction. The features consist of the size of infected red blood cell (RBC), brown pigment in the parasite, and texture using Gray Level Co-occurrence Matrix (GLCM) parts. Finally, the classification method using Multilayer Perceptron (MLP) trained by Bayesian Rules (BR) show the highest accuracy of 98.95%, rather than Levenberg Marquardt (LM) and Conjugate Gradient Backpropagation (CGP) training algorithms.