Blue sharks (Prionace glauca) and oilfish (Ruvettus pretiosus) are frequently caught incidentally in the swordfish surface drifting longline fishery of the eastern Mediterranean Sea. An information theoretic generalized additive model approach, modelling separately: (1) the probability of making a catch; and (2) the positive catch rates, suggested the presence of intra-annual variations in their abundance and revealed interesting associations with some environmental features. Blue sharks were more frequently encountered during late summer in cool water masses. However, the likelihood of making a larger catch peaked in warmer waters through late spring in the vicinity of land. Occurrences of blue sharks were more frequent to the south-west (Ionian Sea), while positive catch rates were higher in the eastern-most regions (Levantine). Oilfish occurrences, as well as catch rates, were always above average to the east. Intra-annual variation was analogous to that of blue sharks. The species showed a preference for cooler water bodies and its distribution was strongly dictated by the lunar cycle. Annual time series showed a decreasing trend of blue sharks abundance. Catch rates for both species depended on fishing gear configuration. Deeper settings (>20 m), more resilient lines and use of fish attractant light-sticks increased the probability of capturing a fish.