Regulations in the maritime sector, with the aim of increasing the energy efficiency of marine power systems, for most of ships (especially for those in international navigation), prescribe mandatory calculations of the Energy Efficiency Design Index (EEDI) and its compliance with the prescribed values.For the time being, coastal ships are not subject to this regulation, but the reduction of their emissions, i.e. the increase of energy efficiency is important due to the reduction of fuel consumption, and thus the reduction of operating costs. Energy efficiency indices in maritime sector are defined as the ratio of carbon dioxide emissions to social benefit (mass of transported cargo, number of transported passengers, vehicles, etc.). In the first part of the paper, an analysis of fishing techniques in the Adriatic Sea was performed. According to the collected data on catch of and fuel consumption, in the period of five years, an analysis of the energy efficiency of seiner ship from the Croatian fishing fleet was made. The possibility of improving energy efficiency was analyzed according to technical and operational measures recommended by the International Maritime Organization (IMO). Based on the collected data, the energy efficiency operational indicator of fishing vessels was formulated. The energy efficiency operational indicator was calculated first, considering diesel engines as the first starters, given the fact that this type of drive is dominant on the vessels of the Croatian fishing fleet. Also, lifecycle emission assessments (LCAs) as well as costs assessments (LCCAs) were conducted for one seiner ship, for a basic diesel engine power system but also for several alternative power system configurations. Finally, a proposal for an economically viable modern solution for improving the energy efficiency operational indicator was given.