By 50,000 years ago, it is clear that modern humans were capable of long-distance sea travel as they colonized Australia. However, evidence for advanced maritime skills, and for fishing in particular, is rare before the terminal Pleistocene/early Holocene. Here we report remains of a variety of pelagic and other fish species dating to 42,000 years before the present from Jerimalai shelter in East Timor, as well as the earliest definite evidence for fishhook manufacture in the world. Capturing pelagic fish such as tuna requires high levels of planning and complex maritime technology. The evidence implies that the inhabitants were fishing in the deep sea.