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Most native forests in Latin America are highly fragmented. In the mid elevation areas of Northern Latin America, the agricultural matrix is frequently composed of coffee. In this region, coffee has been traditionally cultivated under the diverse canopy of shade trees, representing a high quality matrix that can contribute to the social and ecological stability of the region. This agroforestry system has been proven to be important for biodiversity conservation. Studies over the last fifteen years have shown that shaded coffee plantations maintain a high diversity of vertebrates, invertebrates and plants. These organisms play an important role in the functioning of coffee agroecosystems. Shaded coffee plantations promote a high abundance and diversity of natural enemies that help to regulate herbivores, weeds and diseases. Shaded plantations also harbor a higher diversity of native pollinators which have been shown to contribute to higher coffee yields. Likewise, the diverse shade-tree component contributes to soil fertility and soil conservation and has been shown to contribute significantly to carbon sequestration. As a matrix, coffee agroforests also contribute to the conservation of biodiversity withinforest fragments by promoting migration among fragments and facilitating a metapopulation structure. Three "sustainable" coffee certification programs have been developed to help farmers cope with the vagaries of the market: organic, fair-trade and biodiversity-friendly (or shade-grown). Although certified coffees still represent a small niche market, they have the potential to promote conservation and benefit the livelihoods of small producers. Especially under conditions of low international coffee prices, as those experienced in the first years of this century, these certification programs have contributed to the ecological and socio-economic stability of the coffee growing regions of northern Latin America. Inglés