Skipjack tuna is a potential fish resource in the Makassar Strait, Bone Bay, and the Flores Sea waters, Indonesia. This fish is captured by fishermen using many kinds of fishing gear, and the most widely used is purse seine. The study was conducted from January to December 2018, aimed to compare the size structure of skipjack, productivity, and by-catch of purse seine inside and outside of Fish Aggregation Devices (FADs) areas. Fish length (cm, FL), annual production and trips data were collected from 10 ship owners in each fishing area, The main catch and by-catch weight data were obtained through direct observation of 30 trips each for 10 units, both of purse seines inside and outside of FADs areas in each study area. Comparative analysis of the catches of purse seines inside and outside of FADs areas included size structures using the Median Test (T test), productivity and by-catch using Mann-Whitney Test (T test). The results of the study explained that purse seiners inside FADs areas could increase business productivity, but caused an increase in small-sized skipjack and by-catch while purse seines outside of FADs areas caught less small size skipjack, low by-catch but low productivity.