Batbitim marine conservation area (MCA) of Misool, Raja Ampat has been set as an area that is prohibited for fishing activities since 2005. The only activities allowed in that area are tourism and research activities. The difference in the management status between area inside the Batbitim MCA and outside the MCA might affect ecosystem components such as fish and coral reef in the respective area. The present study aims to investigate the ecological status of target fishes in the two areas. Data were collected by using an underwater visual census at 5 sites, in which at each site 3 transects were placed. Collected data are then used to assess ecological indices for the target fishes. It is found that there were 38 species of target fish belonging to 13 families. The diversity index of Shannon was found to be in the range between 0.99 (inside MCA) to 1.67 (outside MCA) and dominance index ranged between 0.26 (outside MCA) and 0.61(inside MCA). The abundance of individual target fish in each location varies between 960 ind ha−1 (outside MCA) and 9413 ind.ha−1 (inside MCA). Those results indicate that there is a discrepancy between the ecological status of the target fish at locations inside and outside the MCA.