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Aim: Woody ecosystems provide critical ecosystem functions and services but are increasingly threatened as invasive pathogens spread globally. Myrtle rust, caused by Austropuccinia psidii, arrived in New Zealand in 2017 and infects at least 12 of 18 species in the susceptible Myrtaceae plant family. Among these are species of structural, successional and cultural importance. We aim to assess whether the functional consequences of Myrtaceae loss could be mitigated if co‐occurring species with shared functional attributes are able to replace them. Location: New Zealand (but with concepts and methodologies that apply globally). Methods: Using a nationwide forest and shrubland plot data set, we assessed community vulnerability to the loss of Myrtaceae species by analysing proportional changes in average trait values when they are absent and produced spatial predictions indicating where species loss might have the greatest impact on community functionality. We then assessed whether compensatory infilling by co‐occurring species would mediate community vulnerability. Results: Forests and shrublands containing Kunzea ericoides and Leptospermum scoparium are highly vulnerable to their loss. Areas most vulnerable overall are the central and south‐eastern North Island, north‐eastern South Island and Stewart Island. For all species, compensatory infilling moderated the impact of their loss. However, if co‐occurring Myrtaceae were unable to respond, possibly if they were also infected, community vulnerability almost always increased because infilling species had different functional attributes, compounding the functional impact. Main Conclusions: Early successional woody plant communities and Myrtaceae‐dominated old‐growth forests are at most risk. Our spatial assessment of species‐level functional impacts from myrtle rust will facilitate better‐informed landscape‐level responses. Management actions and monitoring can now be targeted to areas and communities at greatest risk of losing ecosystem‐level processes. [ABSTRACT FROM AUTHOR]