Tropical anguillid eels are important fisheries and biodiversity contributors across the Indo-Pacific, but their recruitment connectivity remains poorly understood because spawning locations and larval dispersal pathways are largely unresolved. Using genome-wide single nucleotide polymorphisms (SNPs), we quantified species composition, connectivity and kinship among recruiting glass eels collected over four recruitment periods from four rivers in Sulawesi, Indonesia, representing two contrasting coastal systems: Tomini Bay and the Makassar Strait. SNP analyses resolved four genetically distinct species, Anguilla bicolor pacifica, A. marmorata, A. celebesensis, and A. borneensis, demonstrating that the recruitment comprises mixed-species assemblages rather than a single homogeneous cohort. Although species composition varied markedly among rivers and recruitment periods, three species (A. bicolor pacifica, A. marmorata, and A. celebesensis) exhibited negligible genetic differentiation (pairwise FST generally <0.01), moderate genetic diversity, low inbreeding, and large contemporary effective population sizes. Together, these patterns indicate extensive regional connectivity. Kinship analysis identified only ten first-degree relationships, almost all occurring between rather than within rivers, providing no evidence of family-level aggregation during recruitment. In contrast, A. borneensis showed stronger genetic differentiation, suggesting more restricted connectivity than the other species. This represents one of the first genome-wide assessments of tropical anguillid recruitment and demonstrates that fluctuations in assemblage structure primarily reflect changes in species composition rather than genetic subdivision within species. These findings indicate that recruitment dynamics are maintained by extensive regional larval mixing rather than family-based recruitment pulses, providing a foundation for species-specific management and conservation of tropical anguillid fisheries.