Recently, the number of Multinomial Logit (MNL) and Mixed Logit (ML) applications in environmental economics evaluation, in the literature is rapidly growing. The MNL model is the most common used by the researchers. However, the ML model provides a flexible, a straightforward concept and computationally practical econometric method for any discrete choice model derived from random utility maximization. This paper presents the findings from choice everiment (CE) study designed to estimate the economic value of marine ecosystem services in Malaysia. The application of MNL and ML models were used in order to estimate user's preferences of marine ecosystem services. Respondents were asked to select the best among the alternatives of the marine ecosystem attributes which categorized by Marine Parks and Area (MPA) and Ecotourism Facilities and Services (EFS) attributes. The MPA marine ecotourism attributes investigated were ecological management (EM), recreational activity congestion (RAC), provision of employment opportunity to local people (ELP) and conservation charge (CC). Meanwhile, the EFS attributes are accessibility (AC), providing interpretive trails (PIT), providing information (PI) and extra package price (EPP). Results of the study found that the useis are preferred the highest changed in MPA attributes levels compared to EFS attributes levels according to their willingness to pay. Implications of the results will be use in assists policy makers in the developing and managing plan for marine ecosystem services.