The endosymbiotic association between the diatom Hemiaulus and the cyanobacterium Richelia was first observed in the Sea of Marmara in July 2021. The spatial distribution of the host diatom Hemiaulus spp. and the endosymbiont cyanobacterium Richelia intracellularis was investigated along with available physicochemical parameters. Three species of the Hemiaulus genus (H. hauckii, H. membranaceus, and H. sinensis) were morphologically identified in the study area. Hemiaulus hauckii and H. sinensis reached up to 128 × 103 cells L−1 and 38 × 103 cells L−1, respectively, while H. membranaceus was rarely observed. Each Hemiaulus cell contained one Richelia trichome, which had heterocysts at both ends. The surface water temperatures and salinity varied between 23.2°C and 28.5°C, 21.4 and 23.5, respectively. Dissolved oxygen levels ranged from 6.2 to 7.6 mg L−1, while chlorophyll-a concentrations were between 0.3 and 6.8 µg L−1. Nutrient concentrations varied between 0.05 and 0.18 μM for NO3 + NO2–N, 0.04–0.24 μM for NH4–N, 0.02–0.39 μM for PO4–P, and 0.18–1.42 μM for SiO2–Si. This study reveals that the Hemiaulus–Richelia symbiosis may promote the proliferation of diatom populations and may play an important role in nutrient dynamics in nitrogen-limiting environments and in the overall functioning of the marine ecosystem.