PCR-Capillary electrophoresis technology was used to identify diatoms in lung, liver and kidney, and to assess the effects of these diatom species. From 20 randomly selected experimental rabbits, which were drowned in the same location, the liver, kidney and lung from each rabbit were removed and diatom DNA was extracted from the tissues of these organs and subsequently amplified by specific primers of the diatom SSU gene. The diatom DNA was then analyzed using PCR-Capillary electrophoresis. When the amount of biomaterial was increased, the number of diatom species detected in the lung, liver and kidney gradually increased, and was statistically significant (P < 0.01). Bivariate correlation analysis showed a positive correlation between the quantity and types of diatoms. The proportion of diatom species detected in each group varied. When the quantity was greater than 0.9 g in the lung, samples including two or more types of diatoms predominated. When the quantity was greater than 1.5 g in the liver, samples including one or more types of diatoms predominated. When the quantity was greater than 2 g in the kidney, samples which included one or more types of diatoms predominated. The number of diatom species found in different organs with different tissue mass was significantly different, and provides a reference for the detection of diatoms using PCR-Capillary electrophoresis technology. This technique also has potential in the forensic identification of drowning.