The increasing anthropogenic and climatic pressures on marine ecosystems raise concerns about the sustainability of their functions, uses and conservation. Marine megafauna such as marine turtles are particularly vulnerable to these pressures due to their life cycle and the variability of habitats they occupy during their life cycle. Understanding how juvenile population dynamics respond to environmental conditions is crucial for designing effective conservation strategies. The present study investigates whether the genetic composition of juvenile green turtles at recruitment sites changes over time. A total of 346 juveniles were sampled at four key recruitment sites in the South Western Indian Ocean - SWIO (Glorieuses, Mayotte, Reunion and Aldabra) during two sampling phases at an interval between 6 and 17 years depending on the site. Based on mtDNA control region sequences, genetic structures were compared between periods within each site. Even if subtle changes in genetic composition may not be detectable with current genetic resolution, our results suggest that the structure of the juvenile green turtle population has not significantly changed over the course of the study period. Such stability in population structure may be correlated with the stability of regional oceanic currents over the last decades in the SWIO, as well as the dynamics of nesting populations in the different regional genetic stocks contributing in regional juvenile green turtle production.