As malaria elimination efforts continue to show promise, the diagnostic services require constant review to ensure effective treatment. This study was aimed at determining the choice of tools for routine malaria diagnosis in Anambra State. The research was a cross sectional study carried out in 2019 and 2021, using the total population sampling technique to enrol diagnostic centres. Data were collected using pretested questionnaire, and analysed using Mann-Whitney U test, Kruskal-Wallis H test and Chi-square test at a 5% significance level. Microscopy and RDT usage were 73.6% and 68.1% respectively, with 41.8% overlap (p > 0.05). Overall RDT usage was higher, 69.7% than Microscopy usage with 63.6% in Hospital-based Laboratories (p > 0.05). Overall Microscopy usage, ranging from 72.5% to 80.0% was higher than RDT in Private Laboratories, Government-owned Laboratories and Private-owned Laboratories (p > 0.05). SD-Bioline® (38.7%) and Carestat® (35.5%) were the most commonly used RDTs (p < 0.05). Overall usage of thick and thin blood films were: 74.6% and 37.3% respectively, with 11.9% overlap (p < 0.05). Giemsa stain had higher, 78.0% usage in preparing thick blood films than Field stain with 22.0 % (p < 0.05). Usage of Giemsa, Leishman and Field’s stain for thin blood film were: 64.0%, 20.0% and 16.0% respectively (p < 0.05). All the diagnostic centres (100%) report positive and negative results as ‘seen’ and ‘not seen’; with 3.0% of them identifying Plasmodium species while 97.0% report as ‘malaria parasite’ (p < 0.05). Regarding intensity, 1.5% of the diagnostic centres use ‘parasite count / μl of blood’ while 98.5% adopted ‘plus system’ (p < 0.05). Only Microscopy and RDT are used for routine diagnosis of malaria in the study area. However, not all the Microscopy components are used fully and according to standard. Reasons for the choice of tool / their components were given.