Recent studies have shown that the filamentous cyanobacterium Aphanizomenon gracile Lemmermann, strain SAG 31.79, consists of two types of filaments that differ in thickness. These two types are known to vary in resistance to Daphnia magna grazing: thin filaments (<2.5 µm) are more vulnerable to grazing than the thick ones (>2.5 µm). In this study, we investigated whether the difference in the vulnerability to grazing of thin and thick filaments is a result of different thickness of their cell walls, a filament stiffness determinant. We expected thick filaments to have thicker cell walls than the thin ones. Additionally, we analysed whether cell wall thickness correlates with filament thickness regardless of the filament type. A morphometric analysis of cell walls was performed using transmission electron micrographs of ultra-thin sections of the batch-cultured cyanobacterial material. Our study revealed that the thin type of filaments had thinner cell walls than the thick filaments. Moreover, cell wall thickness was positively correlated with filament thickness. TEM (transmission electron microscopy) observations also revealed that the thin type of filaments was often at different stages of autocatalytic cell destruction, which was mainly manifested in the increase in cell vacuolization and degradation of the cytoplasm content. Based on our findings, we assume that previously reported higher resistance of thick filaments to Daphnia grazing results from greater stiffness and excellent physiological conditions of thick filaments.