Background: Highly modified landscapes offer the opportunity to assess how environmental factors influence the integration of alien plant species into native vegetation communities and determine the vulnerability of different communities to invasion. Aims: To examine the importance of biotic and abiotic drivers in determining whether alien plant species segregate spatially from native plant communities or become integrated and lead to biotic homogenisation. Methods: Ordination and classification of a floristic survey of over 1200 systematically located 6 m × 6 m plots were used to examine how plant community segregation, nestedness and homogenisation varied in relation to climate, environmental and human-related factors across Banks Peninsula, New Zealand. Results: The analyses of community structure indicated that native and alien plant communities were spatially and ecologically segregated due to different responses primarily to an anthropogenic impact gradient and secondly to environmental factors along an elevation gradient. Human-land use appeared most strongly linked to the distribution of alien species and was associated with increased vegetation homogenisation. However, despite spatial segregation of alien and native plant communities, biotic homogenisation not only occurred in highly managed grasslands but also in relatively less managed shrublands and forest. Conclusions: The role played by anthropogenic factors in shaping alien and native plant species community structure should not be ignored and, even along a marked environmental gradient, if the recipient sites have a long history of human-related disturbance, biotic homogenisation is often strong.