The emergence and spread of Plasmodium falciparum with resistance to chloroquine (CQ), the safest and cheapest anti-malarial drug, coupled with the increasing cost of alternative drugs especially in developing countries have necessitated the urgent need to tap the potential of plants for novel anti-malarials. The present study investigates the anti-malarial activity of the methanolic extracts of 13 medicinal plants from the Malaiyur and Javadhu hills of South India against blood stage CQ-sensitive (3D7) and CQ-resistant (INDO) strains of P. falciparum in culture using the fluorescence-based SYBR Green I assay. Sorbitol-synchronized parasites were incubated under normal culture conditions at 2% hematocrit and 1% parasitemia in the absence or presence of increasing concentrations of plant extracts. CQ and artemisinin were used as positive controls, while 0.4% DMSO was used as the negative control. The cytotoxic effects of extracts on host cells were assessed by functional assay using HeLa cells cultured in RPMI containing 10% fetal bovine serum, 0.21% sodium bicarbonate and 50 μg/mL gentamycin (complete medium). Plant extracts (bark methanol extracts of Annona squamosa (IC(50), 30 μg/mL), leaf extracts of Ocimum gratissimum (IC(50), 32 μg/mL), Ocimum tenuiflorum (IC(50), 31 μg/mL), Solanum torvum (IC(50), 31 μg/mL) and Justicia procumbens (IC(50), 63 μg/mL), showed moderate activity. The leaf extracts of Aristolochia indica (IC(50), 10 μg/mL), Cassia auriculata (IC(50), 14 μg/mL), Chrysanthemum indicum (IC(50), 20 μg/mL) and Dolichos biflorus (IC(50), 20 μg/mL) showed promising activity and low activity was observed in the flower methanol extracts of A. indica , leaf methanol extract of Catharanthus roseus, and Gymnema sylvestre (IC(50), >100 μg/mL). These four extracts exhibited promising IC(50) (μg/mL) of 17, 24, 19 and 24 respectively also against the CQ resistant INDO strain of P. falciparum. The high TC(50) in mammalian cell cytotoxicity assay and the low IC(50) in anti-malarial P. falciparum assay indicates selectivity and good resistance indices in the range of 0.9-1.7 for leaf extracts of A. indica, C. auriculata, C. indicum and D. biflorus suggests that these may serve as anti-malarial agents even in their crude form. These results indicate a possible explanation of the traditional use of some of these medicinal plants against malaria or malaria-like conditions.