This paper uses value chain analysis as a novel method to examine the conservation status of and strategies for cherimoya (Annona cherimola Mill.), an underutilized, perennial fruit species native to the Andean valleys of Ecuador, Peru and Bolivia. It was found that value chain features such as market channels, chain governance, quality performance and distribution of added value over chain actors differ significantly between cherimoya fruits that are registered by a collective trademark such as the Cumbe variety and another group of more traditionally produced and commercialized cherimoya fruits. The former is exported from its production area (Lima province in Peru) to neighboring Andean countries, is graded and selected intensively, has a higher quality perception and creates significantly more added value for both producers and traders than the other, locally produced cherimoyas whose value chain is governed less intensively. Previous studies on the genetic diversity of cherimoya in the countries of origin have stressed the necessity of conserving cherimoya germplasm in areas characterized by highly diverse (southern Ecuador and northern Peru) or rare (Bolivia) cherimoya germplasm. Although value chain development is generally considered crucial in on-farm conservation of underutilized species, the example of the Cumbe cherimoya shows that intraspecific diversity can be threatened by commercial success. Farmers who believe that quality is exclusively linked to a certain genotype have purchased Cumbe cherimoya grafts from each other, leading to genetic erosion of the local cherimoya genetic base.