Mitochondrial DNA markers have elucidated patterns of connectivity between green turtle nesting populations (rookeries) and juveniles foraging in neritic nursery habitats. However, missing rookery baseline data and haplotype sharing among populations have often impeded inferences, including ascertaining origins of Gulf of Mexico juveniles. We sequenced the mitochondrial control region and additional informative mitogenomic single nucleotide polymorphisms of juveniles foraging in Port Fourchon, Louisiana (LA, n = 127) and Santa Rosa Island, Florida (SRI, n = 47). We collected additional genetic data for previously characterized neritic aggregations in southern Texas (TX, n = 167), St. Joseph Bay, Florida (SJB, n = 174) and southwestern Florida (SWFL, n = 96). We assessed genetic structure among these sites, incorporating published data from a surface-pelagic (SP) aggregation offshore of Louisiana through Florida and a neritic aggregation from the Big Bend region of Florida (BB). We estimated source contributions to aggregations with new genetic data using a Bayesian many-to-one mixed stock analysis (MSA) approach. This data set contains passive induced transponder (PIT) tag number, sampling site information, capture date, control region (CR) haplotype, mitochondrial short tandem repeat (mtSTR) haplotype, and mitogenetic haplotype for each turtle.