Human metapneumovirus (HMPV) has been identified as an important cause of upper and lower respiratory tract disease, affecting individuals of all ages. Seroepidemiological studies have predicted 95% of the global population have been exposed to HMPV by five years of age. Despite the burden of disease, there remains significant caveats in our knowledge of local and global HMPV genetic diversity, likely due to a lack of whole genome sequencing. Prior to this study there was approximately 220 whole HMPV genomes available on NCBI GenBank compared to 155,385 available for Influenza virus and Australian HMPV had not been sequenced in over 15 years. In this study we have generated 160 HMPV whole genomes derived from rescued residual diagnostic extracts from NSW Health. Samples with collection dates between 2013 and 2020 were sequenced for the purpose of this study. Existing and novel sequences were phylogenetically analysed using MAFFT and PhyML with node supports estimated by 100 bootstrap replicates. Molecular epidemiological analysis revealed the co-circulation of multiple HMPV sublineages annually in Australia as well as a distinct change in the distribution of sub-lineages over time, including the dominance of the B strain in recent years and the almost extinction of the A1 sublineage (A2 n=49, B1 n=53, B2 n=54). Notable findings include the identification of a novel 111-nt duplication within the G gene exclusive to the HMPV-A2 lineage, recently identified in Japan, Spain, Vietnam and China, and now in Australia. The post 2016 novel A2 lineage emerged and became the prominent A2 sub-lineage variant detectable in Australia suggesting a possible evolutionary advantage which promotes its wide dissemination. Presented here is a simple and robust approach to complete HMPV whole genome sequencing, with the aim of advancing genomic epidemiological studies and increasing study resolution. Ongoing virus monitoring is imperative to quantify global disease impact, develop tailored disease management strategies and identify large structural changes, such as the one observed in this study.