Aggressive encounters between invasive and native species are considered a key threat associated with the spread of invasive species. Extrinsic factors such as habitat complexity can profoundly influence the outcome of aggressive interactions between conspecifics, and this may also be the case in invasive-native species interactions. This study used invasive and native freshwater crayfish species in Australia as a model system to investigate the influence of habitat complexity on aggression in both intraspecific and interspecific contests. Paired contests between the native Euastacus spinifer and the invasive Cherax destructor were conducted in the laboratory under high and low habitat complexity conditions. Furthermore, the influence of prior residency was examined, with one individual assigned the resident and the other as the intruder. In intraspecific contests, the number of interactions and aggression score were significantly reduced under high complexity conditions; however, complexity had no effect on the time spent interacting and contest outcome. Instead, the two crayfish species differed in terms of time spent interacting. In interspecific contests, complexity had no effect on any of the aggression metrics. Alarmingly, however, we demonstrate that when C. destructor was a resident the likelihood that E. spinifer won a contest fell to a mere 8% compared to 31% when E. spinifer was resident. This study suggests that while habitat complexity plays a role in shaping aggressive behaviour in intraspecific interactions, invasive species are competitively dominant if they are already established i.e. resident in a location and even as intruders. Therefore, preserving habitat complexity in freshwater systems may not be sufficient to sustain populations of native species, and other measures that mitigate the potential for range overlap between the species would also be needed to prevent the further spread of invasive species such as C. destructor within freshwater ecosystems.