Anthropogenic landscape modification can disrupt mutualistic interactions between native plants and soil microbes. Restoration of native vegetation in disturbed habitats may depend upon reconnecting plants with their fungal symbionts, such as arbuscular mycorrhizal fungi (AMF). We compared levels of root colonisation by AMF (arbuscules, vesicles, aseptate hyphae) and dark septate endophytes (DSE; septate hyphae, microsclerotia) between reconstructed and remnant dunes along the southern coastline of New South Wales (Australia) for two native plants: Lomandra longifolia and Carpobrotus glaucescens. Reconstruction was undertaken approximately 30 years ago to reinstate native vegetation and reduce erosion on dunes deforested by European settlers during the 1800s. Fungal colonisation was assessed using the point-intercept method on stained root sections under a light microscope. Root colonisation by AMF did not differ significantly between reconstructed and remnant dune habitats, but did vary significantly amongst sites. In contrast, DSE was two times lower for L. longifolia plants growing in reconstructed compared with remnant fore dunes. Our finding of reduced DSE colonisation in reconstructed dunes may indicate that impacts of land clearing on plant–fungal associations may persist over long time periods for some key plant species. Reduced DSE colonisation may be associated with limited restoration potential and functioning of reconstructed fore dune ecosystems. Future research will be needed to assess the scale of reduced DSE across reconstructed coastal habitats, the role of plant–DSE relationships in vegetation community function, and implications of reduced DSE for ecosystem restoration.