The loggerhead turtle (Caretta caretta) South Pacific subpopulation is classified as 'Critically Endangered’ in the International Union for Conservation of Nature’s Red List, based on its estimated demographic decline. The Southern Province of New Caledonia shelters two distinct major nesting areas for this subpopulation, aggregating approximately 10–25% of all reported nesting activities at the ocean basin scale. A prejudicial knowledge gap subsisted in whether the nesting population of these two nesting areas are part of a single or two distinct Management Unit(s), which could have significant implications for conservation strategies to be implemented. Based on a dataset collected from November 2016 to March 2023, we evaluated the sex-specific connectivity of loggerhead turtles over various temporal scales using three complementary methodologies: satellite telemetry (intra-annual), Capture-Mark-Recapture surveys (inter-annual) and molecular analysis (inter-generations). Our results suggest that reproductive populations from both nesting areas form a unique genetic stock, and that the gene flow is presumably ensured by males, contrasting with the high fidelity to nesting areas shown by females. Considering that both nesting areas show heterogeneous habitat conformations and substantial differences in the associated threat levels, this study highlights the importance to consider both the site-specific aspects and the more global Management Unit scale to ensure a prioritized and coherent conservation strategy. Not considering those aspects could result in management failure and loss of local population segments.