The relationship between silica distribution and microbial colonization in the cuticle of rice straw was examined using scanning electron microscopy and energy dispersive X-ray microanalysis (EDX). Rice straw stems cut into 1 -cm lengths were either treated with 40 g NH3 kg−1 dry matter (DM) or left untreated. Microbial colonization was examined using cultures of Fibrobacter succinogenes S85 grown on rice straw as the sole source of carbohydrate. The nylon bag technique was also used to study the colonization of rice straw by mixed ruminal microorganisms and to determine in sacco dry matter disappearance (ISDMD). Examination by EDX revealed the outer (abaxial) surface of the leaf sheath to be virtually covered by silica, with high levels of accumulation within distinctly arranged opaline bodies (phytoliths). Silica was distributed diffusely over most of the inner (adaxial) surface of the leaf sheath, but phytoliths were absent and some regions were devoid of silica. Ammonia treatment dramatically increased the ISDMD of rice straw, but did not alter the content or distribution of silica on either surface of the leaf sheath. Trichomes contained no silica and were major sites of invasion and colonization in the intact cuticle of rice straw. Cuticular damage and loss were more prevalent in treated than in untreated rice straw, and underlying tissues were found to be devoid of silica and extensively colonized. The improved digestibility of ammonia-treated rice straw may be partially due to a weakening of the adhesion between the cuticle and underlying tissues. Detachment of the cuticle removes this barrier to digestion and exposes underlying silica-free tissues to bacterial colonization.