For a better understanding of soot formation and oxidation processes in conventional diesel and biodiesel spray flames, the morphology, microstructure and sizes of soot particles directly sampled in spray flames fuelled with US#2 diesel and soy-methyl ester were investigated using transmission electron microscopy (TEM). The soot samples were taken at 50mm from the injector nozzle, which corresponds to the peak soot location in the spray flames. The spray flames were generated in a constant-volume combustion chamber under a diesel-like high pressure and high temperature condition (6.7MPa, 1000K). Direct sampling permits a more direct assessment of soot as it is formed and oxidized in the flame, as opposed to exhaust PM measurements. Density of sampled soot particles, diameter of primary particles, size (gyration radius) and compactness (fractal dimension) of soot aggregates were analyzed and compared. No analysis of the soot micro-structure was made. The overall morphology of the biodiesel soot bears similarity to that of #2 diesel, but the soot density, primary particle size, and fractal dimension are smaller for biodiesel.