Accurate diagnosis of malaria helps with adequate treatment and reduction in its transmission. Diagnosis of malaria in Papua New Guinea was largely light microscopy based until 2012 when rapid diagnostic tests (RDTs) were introduced. RDTs are now widely used in Papua New Guinea especially where microscopy sites are unavailable in rural health laboratories, and in emergency situations in hospitals. However, the need for microscopy for parasite density and species identification is of paramount importance in influencing the treatment administered for P. falciparum and non-P. falciparum, including P. vivax. To ensure quality microscopy, the National Malaria External Quality Assessment (EQA) Program monitors the quality of microcopy in country. The performance of laboratories in country was static. One of the main objectives of the Trilateral Malaria Project was to strengthen the diagnosis of malaria in Papua New Guinea. Through the project, a national slide bank is being developed and nested polymerase chain reaction established for malaria surveillance and analysis of samples for the slide bank. Human resource capacity building was achieved in training of more Level 1 and 2 Malaria Microscopists and Scientists who can now perform PCR in malaria in country. Apart from these, Scientists with Clinicians and Data managers from different Institutions were trained in Spatial mapping and molecular diagnostics which are proving as very useful tools. These achievements will definitely improve EQA performance and diagnosis of malaria in routine clinical cases, outbreaks, surveillance and pre-elimination efforts to combat the malaria burden in Papua New Guinea.