Abstract: Munronia pinnata (Wall.) Theob. (Meliaceae) is therapeutically important medicinal plant used for the control of malaria in traditional medicine in Sri Lanka. This study described the cytotoxic potential of five morphotypes and antimalarial activity of the highest cytotoxic morphotype of M. pinnata using brine shrimp toxicity assay and Plasmodium yoelii murin model, respectively. Four concentrations of (0.1, 1, 5 and 10 mg mL-1) aqueous extracts of stem, roots and leaves of five morphotypes of M. pinnata were screened for cytotoxcity using brine shrimp assay. Either, three doses (3200, 1600, 800 mg kg-1) of the whole plant aqueous extract of the highest cytotoxic morphotype of M. pinnata (WPAE) or vehicle or quinine were orally administered for different groups of mice (n = 6) inoculated with P. yoelii murine model. Antimalarial activity was examined in terms of schizonticidal activity and chemo suppression. Overt signs of toxicity, body weight, rectal temperature, stress and aversive behavior were observed with long term oral administration of high dose of WPAE (n = 10). All parts of five morphotypes of M. pinnata showed potent cytotoxic activity. The order of potency was roots>stems>leaves. The highest cytotoxicity exhibited by morphotype collected from Nilgala forest reserve (MGNG3). The high dose of WPAE of MGNG3 has potent oral antimalarial activity. No signs of overt toxicity, signs of stress and aversive behaviour observed during long term toxicological studies. This study showed, for the first time, that all morphotypes of M. pinnata has marked cytotoxcity and morphotype MGNG3 has potent antimalarial activity as claimed by Sri Lankan traditional practitioners.