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Agroecosystems are increasingly recognized as both sources and sinks of non‐native weedy plant species as well as of native plant species, thus management of these systems has important implications for the composition of plant communities and landscape diversity. We quantified the distribution and abundance of both native and non‐native plant species along a habitat gradient representing four management zones: managed agroecosystem, the agroecosystem boundary, ecotone, and neighbouring native forest for two land uses: kiwifruit orchards and neighbouring grassland agroecosystems. Native plant species diversity was highest in forest zones, and declined significantly with increasing non‐native plant diversity across all management zones. The negative relationship between native and non‐native plant species richness and diversity across all management zones was surprising, and contrasts with most ecological literature. Further, non‐native plant species that have the largest ecological or ecosystem impacts were most abundant in ecotones, but were largely absent from managed zones and their margins. Our results suggest that agroecosystems and neighbouring vegetation can harbour native species, but can also be a source of non‐native invasive weeds. These results highlight that agricultural margins contain both native plant diversity and environmental weeds, and that management of these margins affects diversity both on and off the farm.