Alien species may be a valuable resource for marine fisheries, yet their contribution to the catch might be balanced by negative effects on indigenous species. In this study, we explored a unique high-resolution time series of catch data from a highly invaded ecosystem in the eastern Mediterranean. We analyzed over 5000 fishing hauls digitalizing from fishers’ logbooks. We found that the catch per unit effort (CPUE) of alien species increased over time, while for indigenous species, CPUE remained relatively stable between 1996 and 2013. This suggests a lack of competitive exclusion of indigenous target species due to the proliferation of alien species. From the perspective of the fishers’ revenues, alien species gradually became a more important part of the catch, while overall fishers’ revenues showed temporal stability. This was the combined result of alien species increasing CPUE and fishers shifting their effort toward shallower water where alien species were dominant. Our findings demonstrate that alien species can become a valuable resource for a local fishing industry with little effect on indigenous species, which is highly relevant to worldwide fisheries experiencing range redistribution of commercial species.