The malaria burden in Zanzibar has dropped dramatically over the past decade therefore calls for a strict vigilance of laboratory confirmation in all areas of malaria transmission. Malaria diagnosis relies mainly on mRDT and microscopy in public and private health facilities with the main objective of ensuring malaria parasitological diagnosis is performed in a high-quality approach, timely reported with reliable results. In 2003, Zanzibar Malaria Elimination Programme established malaria microscopy quality assurance system in 23 out of 143 public health facilities and 3 selected private health facilities to validate the malaria laboratory quality results. On a monthly basis, 100% of positive slides and 10% of negative slides are collected for slides cross-check. Based on health facility findings, the baseline for malaria sensitivity was ten percent. To date (2017), ZAMEP expanded the scope of work to 98 out 157 laboratory public facilities Unguja and Pemba (77 and 21 respectively), and 26 out of 80 private facilities. The performance of laboratory technicians increased gradually, in which the sensitivity in 2016 was found to be 99.90% whilst the specificity was 99.99%. With regards to parasite species identification, the prevalent species are Plasmodium falciparum (67.9%), followed by P. malariae (13.5%), mixed infection P. falciparum and P. malariae (14.3%) have been detected, and P.ovale (1.8%). Since Zanzibar is moving towards elimination, this intervention helps the program to improve overall malaria case management.