Landscape modification and habitat fragmentation are key drivers of global species loss. Their effects may be understood by focusing on: (1) individual species and the processes threatening them, and (2) human-perceived landscape patterns and their correlation with species and assemblages. Individual species may decline as a result of interacting exogenous and endogenous threats, including habitat loss, habitat degradation, habitat isolation, changes in the biology, behaviour, and interactions of species, as well as additional, stochastic threats. Human-perceived landscape patterns that are frequently correlated with species assemblages include the amount and structure of native vegetation, the prevalence of anthropogenic edges, the degree of landscape connectivity, and the structure and heterogeneity of modified areas. Extinction cascades are particularly likely to occur in landscapes with low native vegetation cover, low landscape connectivity, degraded native vegetation and intensive land use in modified areas, especially if keystone species or entire functional groups of species are lost. This review (1) demonstrates that species-oriented and pattern-oriented approaches to understanding the ecology of modified landscapes are highly complementary, (2) clarifies the links between a wide range of interconnected themes, and (3) provides clear and consistent terminology. Tangible research and management priorities are outlined that are likely to benefit the conservation of native species in modified landscapes around the world.