There is a growing impetus to increase marine protected areas coverage globally from 6% to 30% in 2030. Successfully establishing and maintaining marine protected areas require incorporating public preferences into their establishment and management. We investigate the role of alternate management regimes (top-down and bottom-up) on preferences for marine protected areas and the marginal rate of substitution between natural and man-made capital using a case study in the Asia-Pacific region of Okinawa, Japan. We implemented a choice experiment survey to infer which attributes of marine protected areas are most important for the respondents. We use our survey results to calculate respondents' willingness to support marine protected areas in Okinawa. This study contributes to the policy debate on management of marine protected areas with empirical data that characterizes the perception of Okinawan residents with respect to the role of local coastal communities (bottom-up) compared to central government based agencies (top-down) management. We extend the analysis and estimate the trade-offs to residents in Okinawa between natural capital (i.e. coral coverage and marine biodiversity attribute) and man-made capital (i.e. restrictions on coastal development). We find that the underlying management regime affects the local residents' valuation of the marine protected area with residents showing a higher willingness to support bottom-up management regimes. There is also substantial differences in the willingness to support different characteristics of marine protected areas by management type. Finally, we find that the marginal rate of substitution between natural capital and man-made capital varies by management type such that residents would need to be compensated relatively less in terms of man-made capital in the presence of a policy scenario that proposes an increase in natural capital under a bottom-up management regime.