Capillary electrophoresis (CE) with indirect photometric detection was investigated for the separation of organotin species. Compounds such as dimethyltin (DMT), dibutyltin (DBT), and tributyltin (TBT) are important pollutants in the aqueous environment and techniques are needed to analyze directly aqueous environmental samples quickly and economically. By adjusting the mobile phase to pH 2.65 by HCl, tributyltin, dibutyltin and dimethyltin in aqueous solutions were separated by capillary electrophoresis using indirect ultraviolet (UV) absorbance detection. Pyridine was used as the UV absorption additive at 254 nm and separation was achieved in 6 min. Peak tailing obtained at higher pH suggests strong interaction between the dimethyltin cation and the negatively charged capillary wall. Cetyltrimethylammonium bromide (CTAB) was added to the mobile phase to improve the peak shapes when the pH of the mobile phase was greater than 3.5. Separations of organotin species in mobile phases with or without CTAB were compared. The change of electrophoretic mobility in mobile phases with different pH values indicates that DMT and DBT start to undergo hydrolysis at a pH 3.0. It was also found that the choice of the buffer anions is critical in the separation of the tin compounds as complexes appear to form with DMT and DBT in the presence of oxalate and citrate.