Understanding genetic connectivity and gene flow of long-lived marine species is key for their survival under rising anthropogenic pressure. Indo-Pacific bottlenose dolphins (Tursiops aduncus) inhabit coastal waters of southeast Queensland (SEQ), Australia, a region of intense coastal development, high vessel traffic and subsequent habitat change. Here, we present the first single nucleotide polymorphism (SNP) assessment for this species in Queensland, encompassing the Great Sandy Marine Park (GSMP), the Sunshine Coast (SC) and Moreton Bay Marine Park (MBMP). Pairwise FST values revealed two distinct populations: GSMP was differentiated from a southern SEQ cluster comprising SC and MBMP individuals (FST = 0.02–0.05, p < 0.001). Despite the differentiation, all populations had similar genetic diversity (HO = 0.22–0.23), with no evidence of inbreeding (FIS = -0.00–0.04). Kinship analyses revealed high within-population relatedness (φ = 0.02–0.04), but limited connection between populations. These findings demonstrate the two clusters in SEQ are demographically independent. The southern population encompasses SC into the MBMP, but whether intermediate populations connect GSMP to the southern cluster remains unknown. This study represents a significant advancement in understanding T. aduncus population structure in SEQ and provide a foundation for future conservation management and marine park planning initiatives.