BACKGROUND: The recent emergence of artemisinin resistance in Africa is drawing scrutiny toward the use of alternative anti-malarial therapy based on Artemisia annua and Artemisia afra phytotherapies. This study aimed to determine if either A. annua and A. afra extracts are active against artemisinin-resistant Plasmodium falciparum isolates and determine the selectivity of inhibitory phytotherapies. METHODS: Artemisia extracts were tested in vitro to mimic parasites exposure to extracts in population drinking Artemisia sp. teas. Artemisia extracts were tested in Ring Stage Survival Assays (RSA(0-3 h)) against Cambodian clinical isolates previously genetically and phenotypically characterized as artemisinin resistant or sensitive. Primary human hepatocytes and a human hepatoblastoma cell line (HepG2 cells) were used to assess the cytotoxicity of Artemisia extracts. RESULTS: The study revealed a substantially decreased in vitro activity of A. annua extracts when tested on artemisinin-resistant parasites mutated in the Pfkelch13 gene (RSA(50) 0.137-2.56 g.L(-1)) compared to artemisinin-sensitive parasites (RSA(50) 0.080 g.L(-1)). Conversely, the A. afra extracts have a similar activity on the isolates tested whether they are sensitive or resistant to artemisinin (RSA(50) 0.537-0.758 g.L(-1)) However, the selectivity index for A. afra extracts was much lower than for A. annua extracts (A. afra: 4.628, 4.305 and 6.076 vs A. annua: 387.625, 226.350 and 12.099, respectively for WT, C580Y and R539T). CONCLUSIONS: Artemisia annua activity is driven by artemisinin, implicating the same resistance profiles and concerns associated with semisynthetic artemisinin derivatives. Artemisia afra showed artemisinin-independent antiplasmodial activity. However, the molecular basis of this activity is unknown and may not present a sufficient selectivity, thus further characterization of A. afra is essential.