The deleterious influence of caprylic aicd stress on several weeds have been reported, mainly in the context of the biochemical, physiological and growth parameters of weeds. However, few studies have examined the anatomical and ultrastructural changes in response to caprylic acid. Anatomical injures were observed in Conyza canadensis (L.) Cronquist leaves at 0, 2, 4, 8, 12, and 24 h after 625 μM caprylic acid application in the present study. The initial damage was observed in the mesophyll percentage area and then marginal leaf regions, mid-leaf areas, and the midvein. The accumulation of caprylic acid in the cells, resulted in palisade parenchyma collapse and reduce, cell wall deform, and veins punctual necrosis, was evident in the leaf sprayed with caprylic acid. Chloroplasts and mitochondria in mesophyll cells were disturbed, and followed by markedly reduced photosynthetic activity during caprylic acid application. The leaf anatomy of leaves of C. canadensis treated with caprylic acid displayed time-dependent depletion and disintegration. The degree of changes in the anatomical and ultrastructural leaves of the C. canadensis were studied, suggesting the mechanisms by which caprylic acid act as an effective herbicidal substance.