Marine Transport terms in competition of presenting safer services to its stake holders. The cargo and ship owners are considering the issue as their main concerns. Implementing the ISM Code is a way of achieving  and improving mentioned safety goals. Implementation of these goals, would be in hands of correct operation of the ship’s masters and their crews. Management and responsibility of implementation of the ISM Code would be on shoulder of the ship masters and how they transfer the concept and importance of the Code to their crews. The role of a master is to intermediate between the shipping company and the seafarer and the ship as an individual. Appropriate management of inter relation plays a sensitive role on implementing the ISM Code. In line with the above, there are five categories for implementation of the code which, the following should be taken into consideration; human resource management on board of vessel, training of seafarers, the role of safety management in shipping companies and safety and security matters. These data collection has been carried out from a group of Iranian Ship masters as expertise’s, and the answers  were obtained for the analysis. The role of motivation in improving the implementing of the code has been considered as a challenging point. In the second part of the research, notably the reliability of each part and motivation theory, has been taken into the consideration. To analyze the collected data, the SPSS 16 and AMOS software’s were utilized. The collected statistics showed that implementing of ISM Code by the Iranian seafarers is realized and the calculated amount of chi-square and the degree of freedom (df) indicates the virtually of the research. Therefore, implementation of the ISM Code along with motivation would have a positive effect in the safety on board of the ships and would result in the safety of navigation for Iranian seafarers.