Perhaps the most understudied ecosystem services are related to socio-cultural values tied to non-material benefits arising from human–ecosystem relationships. Bequest values linked to natural ecosystems can be particularly significant for indigenous communities whose livelihoods and cultures are tied to ecosystems. Here we apply a discrete choice experiment (DCE) to determine indigenous fishers’ preferences and willingness-to-pay for bequest gains from management actions in a locally managed marine area in Madagascar, and use our results to estimate an implicit discount rate. We validate our results using a unique rating and ranking game and other mixed methods. We find that bequest is highly valued and important; respondents were willing to pay a substantial portion of their income to protect ecosystems for future generations. Through all of our inquiries, bequest emerged as the highest priority, even when respondents were forced to make trade-offs among other livelihood-supporting ecosystem services. This study is among a relative few to quantify bequest values and apply a DCE to model trade-offs, value ecosystem service flows, and estimate discount rates in a developing country. Our results directly inform coastal management in Madagascar and elsewhere by providing information on the socio-cultural value of bequest in comparison to other ecosystem service benefits.