Migratory species often spend the non-breeding season in areas that differ in both distance from the breeding grounds and habitat quality, which can cause a segregation of the population. In sexually dimorphic species, differential energetic requirements and foraging strategies of each sex can lead to the use of different non-breeding grounds. However, because migratory birds use very distant and often hard to access habitats, it is often difficult to systematically assess a population's adult sex ratio (ASR) over time and across sites to get insights into sexual segregation. Here we study a long-distance migratory shorebird, the Hudsonian Godwit Limosa haemastica, to explore the ASR in two separated bays at Chiloé Archipelago (41°S, Chile) and evaluate potential segregation of the sexes within this population during the non-breeding season. Using a molecular approach, we developed a standardised criterion to accurately sex the individuals based on their bill length. With this criterion we were able to sex 92% of the sample (n = 265), with the remaining corresponding to birds in the overlapping range of bill lengths that needs to be sexed molecularly. We found that this godwit population, which breeds in Alaska, does not present a large-scale sexual segregation between non-breeding sites but is overall male-biased (ASR = 0.59). Interestingly however, there were significant differences in ASR between bays that were maintained throughout three consecutive non-breeding seasons. Further studies are needed to estimate potential consequences of these local differences in ASR on the population dynamics of this interhemispheric migratory species.