Invasive Caulerpa species pose significant threats to marine ecosystems globally. In the Hauraki Gulf, Aotearoa recent outbreaks are raising concerns due to their detrimental effects on local biodiversity and cultural practices. This study addresses priorities expressed by Māori iwi and hapū (tribe and subtribe) regarding the impacts of invasive Caulerpa. Through a thematic analysis of Māori perspectives two research questions were developed, (1) understanding relationships across invasive and native Caulerpa, and (2) investigating chemical constituents affecting native biodiversity. Using a molecular taxonomic approach, the two invasive Caulerpa species in Aotearoa were confirmed as genetically distinct but morphologically near indistinguishable. Alongside this, a potentially new native species was identified. Organic chemistry techniques revealed the presence of caulerpin and preliminary evidence for caulerpenyne, two highly active compounds, in invasive Caulerpa, indicating a novel area of research. Our findings emphasize the importance of integrating Māori perspectives to guide research for the benefit of indigenous communities. Furthermore, they highlight the urgent need to document and protect local biodiversity threatened by invasive Caulerpa. This study contributes to a deeper understanding of the environmental, cultural, and social impacts of invasive species, informing future conservation efforts and management strategies guided by Māori perspectives in Aotearoa.