Coloured pan trapping is a simple and efficient method for collecting flying insects, yet there is still discussion over the most effective bowl colour to use for particular target groups (e.g. pollinator insects). The success of particular colours can vary across bioregions and habitats. Most published pan trap studies have been conducted in the northern hemisphere, and very few investigated the effects of habitat on pan trap catches. Our study is one of the first to (1) sample for potential pollinators in Australian mallee vegetation and almond orchards and (2) investigate whether habitat interacts with trap colour to influence pan trap catches. We sampled Hymenoptera and Diptera using yellow, white and blue pan traps in native mallee vegetation and two types of managed almond orchards (monoculture and plant-diverse) in the Murray Mallee bioregion of north-western Victoria, Australia. Yellow traps caught the most insects across all habitats, although catches in each colour trap varied with habitat. For all insect groups combined, blue traps caught more individuals in mallee habitats than in almond orchards. For native hymenopterans, yellow traps caught more individuals in plant-diverse orchards than in native sites, while blue traps caught more individuals in native sites. Our results highlight the importance of considering the habitat of individual pan trapping surveys, as no one trap colour is likely to be suitable for trapping target insects across all habitats.