By the mid-1900s the guanaco (Lama guanicoe) approached extinction in southern South America due to habitat destruction and hunting. In order to maintain the ecological prominence of this iconic species, as well as assist in the management of populations that are emerging economically while increasing in conservation value, accurate and potentially rapid estimates of effective population size (Ne) (demographic and/or genetic) are essential. Estimates of Ne generally focus on the genetic effective population size; however, we posited that both parameters may be necessary to provide more accurate and timely estimates. Therefore, we examined the performance of three demographic and four genetic estimators of Ne of guanacos in Torres del Paine National Park, Chile, at different years and time intervals between 1987 and 1997. We compared our estimates with census estimates of the adult population size (Nac) during the same time period. Average Ne/Nac ratios of demographic estimates varied between 0.04 and 0.99 of the adult census size. Genetic estimates varied between 0.02 and 0.08 of the adult census size. Based upon group composition and population size (n = 82) of guanacos in 1975, the number of breeding adults was 44 animals. Mean Ne of the single-sample and temporal genetic estimators was 43.1, and 34.3, respectively; estimated Ne of one of the demographic estimators was 41. Our findings suggest that intermittent genetic estimates of Ne (via fecal samples, carcasses, blood collection during capture, and/or other non-invasive methods) can provide crucial information regarding the genetic integrity of increasingly isolated populations of wild South American camelids. Considering the overall performance of these estimators, and differences in how each functions, we recommend an integrative approach using both genetic and demographic estimators, to evaluate Ne for the wild South American camelids and other species with polygynous mating systems.