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African animal trypanosomosis is a debilitating tsetse-transmitted parasitic disease of sub-Saharan Africa. Therapeutic and prophylactic drugs were introduced more than 50 years ago, and drug resistance is increasingly reported. In a cross-sectional study, 467 cattle were microscopically screened for trypanosomes. Samples were collected in May-July 2014 from five villages (Botao, Mungama, Zalala-Electrosul, Zalala-Madal, and Namitangurine) in Nicoadala district, Zambezia province. To evaluate treatment efficacy, trypanosome-positive animals in each village were randomly assigned to two groups, one treated with 0.5 mg/kg b.w. isometamidium (Inomidium®), the second with 3.5 mg/kg b.w. diminazene (Inomazene®). Cattle were microscopically monitored at days 0, 14, and 28 post-treatment. At day 28, trypanocides were swapped to investigate single or multiple resistance. Microscopically negative samples from the monitoring days were tested using 18S-PCR-RFLP. 22.9% (107/467) was found positive on day 0. On day 14, nine animals in Botao and seven in Mungama were positive. On day 28, in Botao, four animals from the diminazene group and four from the isometamidium group were positive. In Mungama, four animals from the diminazene group were positive on day 28. On day 42, six animals (9%) in Botao and two (9.5%) in Mungama remained positive after drug swap. No relapses occurred in Namitangurine. The 18S-PCR-RFLP consistently detected more positive than microscopy: indeed, positives reached 12, 13, and 8 in Botao and 9, 7, and 4 in Mungama, at days 14, 28, and 42, respectively. Single- and multi-drug resistance in Nicoadala district, Zambezia province, is thus here confirmed. This should be considered when choosing control options.