Seagrass diversity along the Tanzanian coast has been documented mainly through morphology, with limited molecular reference data available for Tanzania and the wider Western Indian Ocean. This study combined morphological identification with nuclear ribosomal internal transcribed spacer (ITS) and plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) markers to assess species diversity and molecular relationships of Tanzanian seagrasses. Field surveys identified 12 seagrass species, and 84 ITS and 116 rbcL sequences were analysed alongside Indo-Pacific reference data. ITS distinguished all morphologically identified species, whereas rbcL distinguished only 10 and failed to distinguish closely related species within Halophila and Halodule. Molecular analyses confirmed that morphology is reliable for most species but identified recurrent misclassifications among morphologically similar species. Tanzanian sequences clustered with broader Indo-Pacific lineages, indicating limited regional divergence. These findings strengthen molecular reference libraries for the Western Indian Ocean and provide a foundation for future taxonomy, biodiversity monitoring, metabarcoding, and environmental DNA applications.