The usage of CFC and HCFC gases, which are extensively used in ship refrigeration and air conditioning systems, has been restricted due to harmful effects on the ozone layer and global warming. Thus, the use of alternative refrigerants becomes a possible solution. In this study, the performance parameters, environmental and economic effects of the system for various refrigerants were analyzed comparatively for marine refrigeration systems. For this purpose, the refrigerants R407C, R1234yf, R245fa, R152a, R513a, R450a, R161, R453a, and R717 are investigated as alternatives to the most commonly used R22 and R134a refrigerants on board ships. The results show that the best alternatives -in terms of performance, environment and economy- for R22 are R717 (new) and R453A (drop-in) and for R134a are R717 (new) and R152a (drop-in). In addition, drop-in, retrofit or new system suitability of the analyzed refrigerants for replacement of R22 and R134a are presented.