Perennial tree crops are often grown in complex multistrata systems that incorporate natural vegetation.These systems contribute simultaneously to sustaining rural livelihoods and to the conservation ofbiodiversity, but their productivity is usually low. Introduction of high yielding germplasm, usually selectedin monocultural plantations, is a potential way to increase productivity, but a critical requirement is thatsuch plants can be established in a competitive multispecies environment. The establishment of clonalplanting stock in the jungle rubber agroforests of Indonesia was explored through participatory on-farmresearch. The trial involved four farmers who grew clonal rubber trees in a total of 20 plots, constitutingfive replicate experimental blocks spread across four farms. Unexpectedly, vertebrate pest damage bymonkeys (Presbytis melalophos nobilis) and wild pigs (Sus scrofa) was the most important influence onestablishment, explaining almost 70% of the variation in rubber tree growth. The amount of labour investedin weeding was also positively correlated with rubber tree growth. Farmers generally decided tocompletely cut back vegetation between rows of rubber trees, including potentially valuable trees, ratherthan weeding within the rows and selectively pruning trees in the inter-row. Farmers thought that theinter-row vegetation would harbour vertebrate pests and compete with the clonal rubber, and they hadaccess to fruits, firewood and other non-timber forest products from other land. Thus, contrary toexpectations, when offered clonal germplasm, farmers opted to use plantation monoculture methods toprotect what they considered a valuable asset, rather than maintain the traditional multispecies strategythey use with local germplasm.