Policies for promoting the in situ conservation of underutilized crop varieties include the provision of economic incentives to farmers for their market commercialization. Nevertheless, market participation could also have the counter-effect of favoring the cultivation of uniform commercial crop varieties and inducing the erosion of crop genetic diversity. The objective of this research was to identify the determinants of the in situ conservation of native chili varieties, including market participation. To this end, 128 farmers were surveyed in the Amazon rainforest region of Ucayali in Peru. The data were analyzed using probit, multinomial logit and truncated Poisson models with covariance matrix correction for cluster errors by rural community. Results suggest that participation in commercial agriculture statistically significantly increases the in situ conservation of native chili varieties; only when farmers sell their products to local retailers, but not when they supply wholesalers. In particular, this result implies that policies designed to encourage specific forms of market participation could have a positive effect on farmers’ economic well-being and simultaneously could help to achieve crop genetic diversity conservation goals.