Seawater salt deposition was investigated in the needles of Pinus thunbergii trees growing in the coastal area of Pohang, Korea. Both green asymptomatic and brown necrotized needles were air‐dried and processed for field‐emission scanning electron microscopy and X‐ray microanalysis. Seawater salt crystals appeared randomly deposited on the asymptomatic needles. No distinct epicuticular waxes were found in the stomata or on the needle surface. The salt crystals, which varied in size, were observed in the stomatal chambers as well as on the apertures of the Florin rings, and similar crystals were also observed on the necrotized brown needles. Sodium (Na) and chloride (Cl) were prevalent on the needles and mostly co‐localized in the crystals. Magnesium was partially co‐localized with Cl, but often co‐occurred with potassium. Depending on the elemental composition of salts, two types of salt deposition were observed on the needles: (i) the coffee‐ring pattern and (ii) the uniform pattern. The apparent NaCl crystal depositions in the stomatal chambers indicated the stomatal penetration by seawater and solutes in the seawater‐sprayed needles of P. thunbergii. These results provide insights into the initial phase of seawater salt‐induced injury occurring through the stomatal pathway in pine species distributed in coastal areas.