Successful Fisheries Management should be constructed upon accurate data to evaluate the fisheries stock correctly. Meanwhile, efficient monitoring system is required to oversee the execution of policies. Observer Program which is the most effective method to understand the data of fisheries was promoted since 2001 in Taiwan. However, due to the different values, roles, living habits between observers and captains, they still have conflicts. Amount 50 scientific observers, 25 randomly selected for the survey during October to December in 2008. The interview focus on five major subjects: (1) report of fishing activities; (2) Bycatch; (3) Biological sample collection; (4) Living area; (5) Daily schedule. The conflict factors and the conflict points between observers and captains were discussed (with qualitative and quantitative methods) in the research. It reveals that the most significant element leads to conflicts is relating Bycatch¡F88% (22 persons) of the reviewed observers reported conflict in this issue, and the main reason is the profits of shark fin. Besides, there are 20 observers, which is 80% of the sample, mentioned that Logbook is another factor leads to arguments of commercial benefits. Furthermore, 16 persons (64%) also agree that Biological sample collections is another factor; the main reason is the otolieh sampling will destroy the price catch. Finally, it shows that few observers chose Activity area and Living habits, which only have 12% (3 person) and 24% (6 person) respectively. In addition, in the factors of Logbook and Bycatch, the conflict level is effected by educational degree of observers. This research also investigates the opinions of observers, which could improve the relationship within the industry. To sum up, the study has reviewed and integrated available researches to deal with conflicts in Fisheries management. The findings of this research could be applied in setting up fisheries policies.