Objective To evaluate the detection capability of the malaria laboratories at all local levels in Hubei Province, the provincial malaria diagnosis reference laboratory re-examine the reserved blood samples of imported malaria cases sent from local malaria laboratories at all levels, and the results produced by local and provincial laboratories were analyzed for capability evaluation. Methods Information of imported malaria cases including the diagnosis institution, diagnosis outcome and the samples reserved in 2016—2020 in Hubei Province. The diagnosis institution was analyzed descriptively. The reserved blood samples from local malaria laboratories were checked by Hubei Provincial Malaria Diagnosis Reference Laboratory through microscopy and nested PCR, and the coincidence of malaria positives and parasite species between local laboratories and provincial laboratory were compared, and analyzed. Results From 2016 to 2020, a total of 608 imported malaria cases were reported in Hubei Province, among them 89.5% (544/608) were diagnosed in medical institutions, 10.5% (64/608) in CDCs, with 54.6% (332/608) being diagnosed in district (city)-based medical institutions. From 2016 to 2020, the proportion of medical institutions in the malaria diagnosis units were 84.1% (132/157), 84.4% (92/109), 90.4% (122/135), 95.2% (157/165) and 97.6% (41/42) respectively (χ² = 16.815, P < 0.05), The Hubei Provincial Malaria Diagnosis Reference Laboratory re-examined 604 reserved samples, of them 92.4% (558/604) were diagnosed as malaria in local malaria laboratories, of them 88.5%（494/558） were recorded with correct identification of parasite species. Over the years checked, the coincidence rates between locals and province in Plasmodium positives and parasite species identification were 82.9% to 96.2% and 79.4% to 94.4%, respectively, with the difference being statistically significant (χ ² = 9.273, 13.787, P values < 0.05); the coincidence rates of malaria diagnosis and parasite species identification at medical institutions were(93.2%, 503/540; 89.5%, 450/503), which were higher than that of CDCs (85.9%, 55/64; 80.0%, 44/55). The coincidence rates of malaria diagnosis and parasite species identification at the provincial, city, county and township medical institutions were (100%, 100%), (93.3%, 88.3%), (90.2%, 86.4%) and (11/14, 9/11) respectively, showing a trend that the higher the level of medical institutions, the higher the correctness rat of diagnosis (χ ² = 13.092, 15.598, P < 0.05). The coincidence rates in identification of P. falciparum, P. vivax, P. malariae, P. ovale and mixed infection identification were 96.9%, 96.0%, 62.5%, 48.8% and 0, respectively, with significant difference(χ ² = 132.880, P < 0.05). Conclusion The diagnosis of malaria cases were made mainly in medical institutions in Hubei province. Overall, the local malaria laboratories show comparatively high detection capability, however the parasite species identification other than P. Falciparum remains to be improved.