Connectivity between populations plays a key role in the long-term persistence of species in fragmented habitats. It is an issue of concern for the preservation of biodiversity in drylands since landscapes in water limited environments are characterized by low habitat cover, high habitat fragmentation and harsh matrices, and are being rapidly degraded at the global scale. In this study, we modelled landscape connectivity between the 11 remnant coastal and Andean populations of the guanaco Lama guanicoe, an emblematic herbivore indigenous to South America, in Chile's arid Norte Chico. We first produced a habitat surface model to derive a regional surface resistance map; and we then used circuit theory to map functional connectivity, investigate the degree of isolation of the populations, and identify those that most contribute to the network patch connectivity. Predicted suitable habitat for L. guanicoe represented about 25% of the study region (i.e. 29,173 km2), and was heterogeneously distributed along a continuous stretch along the Andes, and discontinuous patches along the coast. As a result, we found that high connectivity current flows in the mid and high Andes formed a wide continuous connectivity corridor enabling connectivity between all the high Andean populations. Coastal populations, in contrast, were predicted to be more isolated. They only connect to medium and high altitude populations, and for two of them, animal movement was linked to the effectiveness of wildlife crossings. Based on the degree of connectivity, population size, and local threats, the coastal and the northernmost populations were identified as being most vulnerable, while the Andean populations appeared to be least at risk, even when located near areas of mining activity. Collectively, our results suggest that functional connectivity is an issue of concern for L. guanicoe in Chile’s Norte Chico, and that future conservation and management plans should adopt a landscape strategy aiming at conserving the functional connectivity between the coastal and Andean populations, and at protecting the habitat patches likely to act as stepping stones within the connectivity network.