The clonal and genetic diversity of clonal plant populations provides insights in their capacity to resist and recover from disturbances. Despite the need to include diversity estimates in ecosystem monitoring and management, there is limited understanding of the temporal patterns of diversity in clonal plants, especially for colonising species. This study assessed temporal patterns in clonal and genetic diversity and community composition of the colonising/opportunistic seagrass Halodule uninervis over short (6 months) and longer term (4-6 years) timeframes along ~1000km of West Australian coastline across a range of disturbance conditions. Clonal and genetic diversity showed remarkable temporal stability over both timeframes for all populations, despite temporal changes in community composition. This is likely due to irregular sexual reproduction, persistent dispersal barriers between populations and intermediate levels of disturbance. Finally, despite the life history of H. uninervis, 19% of genets persisted over 4-6 years, and we estimated a clonal age up to 3905 years, which is comparable to that found in persistent seagrasses. Both the temporal stability in diversity and the persistence of individual genets, illustrate opportunities for restoration of seagrass meadows through the introduction of new genets and the need for inclusion of clonal and genetic diversity in seagrass monitoring.