Theories to explain the success of alien species often assume that they are inherently different from native species. Although there is an increasing body of evidence showing that alien plants tend to dominate in highly human-modified environments, the underlying reasons why widespread natives might differ in their habitat distribution have rarely been addressed. We used species distribution models to quantify the dominant environmental axes shaping the habitat of 95 widespread native and alien herbaceous species in a highly modified grassland-dominated landscape in New Zealand. For each species, support vector machines were used to determine 1) the environmental variables that most strongly determined a species’ distribution; 2) the affinity towards a particular position along environmental axes; and 3) tolerance to environmental variation. These three measures were compared among native perennials (n = 31), alien perennials (30) and alien annuals (34). Independent of their origin, species’ distributions were defined by similar environmental variables. Nevertheless, native and alien species occupied different regions of the dominant environmental axes. Perennial natives occupied regions associated with lower human disturbance, while perennial aliens were associated with habitats that had been modified by vegetation clearance, pasture development and livestock grazing. Annual aliens differed from perennials and were associated with both semi-natural and more intensively managed vegetation. No evidence was found that aliens had broader environmental tolerances than natives that might facilitate invasion into a wider range of environments. Thus, widespread native and alien species differ in the degree to which environmental factors shape their distribution as a result of anthropogenic perturbations to which they respond differently as well as the introduction of functional groups that are capable of exploiting novel environments.