Diagnostics play a crucial role in the elimination of malaria. For elimination, the World Health Organization recommends confirmation and speciation of malaria cases to guide and monitor surveillance, treatment, and severity. With a prevalence below 1% and less than 5,000 cases in 2018/19, Zanzibar examined SD BIOLINE Malaria Ag Pf/Pan mRDT and microscopy to assist in surveillance. While mRDTs are useful in typical clinic conditions for identifying positive cases, microscopy is needed for speciation. Like most of East Africa, Zanzibar is endemic for Plasmodium falciparum, but between 2017 and 2018, the Zanzibar observed the presence of other plasmodium species. ZAMEP determined the magnitude of other species by microscopy based on an analysis of positive mRDT patients. A convenience sample of 23 clinics in Unguja and Pemba Districts was selected based on ability to transport blood smear slides within 24 hours of collection to laboratories. Health workers at the facilities and District Malaria Surveillance Officers were trained and prepared blood smears from positive mRDT cases. Two trained microscopists using Olympus microscope reviewed 203 slides based on positive mRDT results. Microscopy found 182 positive slides of which the geometric mean parasite density was 14,995/μL parasites with a range of range 64 to 556,750. Among these 182 positive blood slides, 94% revealed P. falciparum. There was one case (0.5%) of P. ovale. P. malariae findings consisted one case of this parasite alone (0.5%) and 6 cases (3.3%) of mixed infection with P. falciparum. The remaining 3 cases were P. falciparum sexual forms. The two microscopists had an agreement level of 100%. The study demonstrated that ZAMEP is capable of monitoring malaria species as it moves toward elimination. The low level of non-falciparum species and the specific lack of P. vivax implied that national malaria treatment guidelines using ACTs should be adequate.