Agroforestry systems maintain intermediate levels of biodiversity between natural forests and purely agricultural land-uses and may therefore increase connectivity or sustain biodiversity in fragmented forest landscapes. This hypothesis is tested by comparing the species richness and similarity in species composition between forest fragments and agroforestry systems in two landscapes in Guatemala. Connectivity indices were calculated based on the similarity of biodiversity held between forest and agroforestry. Tree and ant species richness was significantly higher for forest than agroforestry land-uses. Conversely, species richness of leaf hoppers (Cicadellidae) was lower in forests compared to agroforests. Chao-Sorensen estimates indicated a high proportion of ant species were shared (0.78–0.99) between different agroforestry land-uses and forest fragments, but lower proportions of tree (0.39–0.55) and leaf hopper species (0.42–0.65). Including the contribution of agroforestry systems in estimates of forest connectivity, based on their biodiversity relative to forest, substantially increased the land area rated with high connectivity (by 100–300%) and forest edge connectivity (by 70–170%), but had negligible impact on land area rated as dense forest. The major forest fragments in the two landscapes were linked by land rated as medium connectivity for forest biodiversity. Thus, agroforestry contributes to the capacity of the landscape to support biodiversity, but only partially increases connectivity between forest fragments in the two landscapes studied. If these benefits are to be sustained, consideration needs to be given to the incentives for land-owners to maintain agroforestry systems.