One of the most critical issues in the worldwide shipping industry that has been in the point of interest of the ship owners is the vessels’ flag selection process and the ship registry. This research paper aims to determine the meaning of the “Flag of Convenience”, its particular characteristics and its role in the global shipping market. Specifically, it investigates whether the Flags of Convenience are more advantageous for a shipowner or not and identify their comparative advantage over National Flags. Through a quantitative analysis, a comparison has been made between two of the most significant Flags of Convenience, the Maltese, and the Liberian flags. Firstly, the operational costs of the Containerships, the Bulk carrier vessels and the Tanker vessels of the Liberian and the Maltese flags, for the fiscal year 2018, have been analysed. Following, the individual elements of the operating expenses were recorded in order to go deeper into the analysis. More specifically, the relevant crew costs, the stores and lubricants, the repair and maintenance, the insurance and administration costs have been recorded for the three aforementioned vessel categories for the Liberian and Maltese flags for the year 2018, from data received through the Maritime Moore Index. The results produced from the analysis of this research suggest that for the year 2018, it would be more beneficial for a shipowner whose fleet consists of Container vessels and Tanker vessels fleet to register the vessels under a Liberian flag, while for shipowners with Bulk Carrier vessels to register their vessels under the Maltese flag. These results, partly explain why shipowners end up registering their vessels under a specific flag.