Abstract The Southwest Atlantic (SWA) is an important region for the Caretta caretta characterized by unique genetic lineages; however, their life history is still misunderstood. In this study, we evaluated the demographic patterns of four SWA rookeries using D-loop and microsatellites data looking for expansion and bottlenecks signals. Then, we simulated several colonization scenarios for the SWA using Approximate Bayesian Computation. The best-supported scenario indicated that loggerheads might have colonized the SWA region once by the ancient lineage of ES/k4 that signals a sharing ancestry history, and from it originated the other lineages by divergence and introgression processes, explaining the high admixture levels between their rookeries and genetic clusters. The D-loop recovered population stability in the past, but microsatellites identified sharp recent bottleneck events, which may have been triggered by the Last Glacial Maximum, El Niño Southern Oscillation, and anthropogenic actions. Thus, we provide, for the first time, a complete assessment of the life history and colonization of loggerhead into the SWA, demonstrating differences between markers (matrilinear and biparental) that may bias our understanding of their genetic and demographic patterns, and which should be considered for conservation programs at a global scale.