The COVID-19 outbreak in Malaysia was initially categorized according to clusters such as first wave, second wave, third wave, etc. However least that we know if the virus that causes these clusters were all the same or had mutated and become more virulent. Hence, this study was conducted from 2020-2021 before the commencement of COVID-19 GENOME CONSORTIUM to characterize the novel coronavirus known as SARS-COv-2 via full genome sequencing. Viral RNAs were extracted from respiratory samples from 100 COVID-19 cases encompassing 1st wave till 3rd wave of the pandemic and characterized using next generation sequencing (NGS) platform. It was found that the early outbreak strains belong to the Wuhan B lineage after which it evolved throughout the 2nd and 3rd wave. During the 2nd wave, there were the emergence of the D614G mutation observed in the Sivangangga and Kedah clusters and subsequently dominated all other lineages. During the commencement of the 3rd wave, a distinct lineage called Malaysian B.1.524 was discovered. This lineage was first identified in the Benteng Lahad Datu cluster and dominated COVID-19 cases in Peninsular Malaysia too for approximately 9 months prior to the emergence of variant of concerns. The phylogenetic analysis revealed a vast evolution comprises various lineages, some which dominated and some existed for short span of time and mutations that mainly occurred in the spike protein region. This reflected that the virus had undergone adaptation to continue it’s survival and confer fitness.