A longline experiment consisting of 45 paired sets (90 sets total) was carried out to evaluate a technique which maintains target catch rates while reducing non-target catch rates. Control sets were compared to experimental sets which eliminates the shallowest hooks (∼less than 100 m depth). Researchers hypothesized that by eliminating shallow hooks, target catch of deeper dwelling species such as bigeye tuna ( Thunnus obesus) would be maximized while incidental catch of many other non-target, but marketable epi-pelagic species (e.g. billfish), bycatch (discards) of other fishes and elasmobranchs, and protected sea turtles and marine mammals would be simultaneously reduced. To control for differences in fishing power, gear, and deployment techniques; a single vessel was contracted to perform all 90 paired longline sets (45 experimental sets using no-shallow-hooks and 45 control sets using standard methods). Control sets consisted of longlines that were suspended by floats on typical 30 m long floatlines in catenary-type shapes that fished a range of depths, determined by temperature–depth recorders (TDRs) to be 44–211 m (27.5–11.2 °C). By contrast, elimination of shallow hooks in the upper 100 m of the water column (hereinafter referred to as experimental sets) was achieved by suspending the fishing portion of the mainline on 75-m long, 3 kg weighted vertical sections of mainline suspended by floats on 30 m floatlines. As determined by TDRs, this arrangement ensured that all hooks fished at depths >100 m (103–248 m; 24.8–11.3 °C). Thirty percent of hooks in control sets fished at depths less than 100 m while all hooks on experimental gear fished greater than 100 m. Because many factors influence catchability, longline sets are by nature multivariate, and statistical comparisons were made between the two set types using canonical discriminant analysis (CDA). Except for the depth of shallow hooks, operational characteristics between experimental and control sets were the same. The catch rates of bigeye tuna were similar on the two sets types but the catch rate of sickle pomfret ( Taractichthys steindachneri) was significantly higher ( p = 0.011) in the experimental sets as compared to control sets. However, statistically fewer wahoo ( Acanthocybium solandri, p = 0.019), dolphinfish ( Coryphaena hippurus, p = 0.008), blue marlin ( Makaira nigricans, p = 0.001), striped marlin ( Kajikia audax, p = 0.018) and shortbill spearfish ( Tetrapturus angustirostris, p = 0.006) were captured on the experimental sets; thus longline interactions and impacts on these species were reduced with the experimental gear. The reason for the differences in catch rates between gear types is likely due to the vertical habitat preferences of the species involved; interactions with epi-pelagic species with shallow distributions in the uniform mixed layer were reduced by deploying hooks greater than 100 m. By logical extension, the experimental gear will also likely reduce interactions with sea turtles. Except for additional lead weights, floats, and floatlines, only slight modification of existing longline fishing gear and methods were required to deploy the experimental gear. The main drawback of this method was the increase in time to both deploy (≈0.5 h) and retrieve (≈2 h) the gear. Knowledge of species vertical distribution patterns can play an important role in modifying fishing gear to reduce bycatch and can also assist managers in regulating fishing practices with a higher degree of likelihood of predicting catch rates and species captured in different gear types.