The removal of Reactive red 43, as a model pollutant, and some organic dyes with different structures by electrocoagulation process was investigated using iron (EC‐Fe) and aluminum (EC‐Al) anodes to explain dyes removal mechanism differences in EC‐Fe and EC‐Al processes. First, the effects of current density, electrolysis time and pH on the removal of Reactive Red 43were studied. The maximum removal efficiency (RE) was obtained in relatively acidic medium (pH = 4.25) in the first 12 minutes of EC‐Al. While, in EC‐Fe, a significant lag time between the starting of the process and initiation of considerable dye removal was observed. The color RE was supplemented with determining the RE of chemical oxygen demand. The COD values were determined for decolorization of solution containing 50 mg/L of RR43 and after 24 min of processes when the applied current density to monopolar batch electrochemical reactor was 25 A/m2. The COD removal efficiencies for the mentioned conditions were 73.92% and 97.12% for EC‐Al and EC‐Fe processes, respectively. The kinetics studies were carried out for both EC‐Al and EC‐Fe processes. In the similar operational conditions, the removal of basic dyes was not considerable by EC‐Al. However, the RE of anionic dyes was improved with the addition of the number of sulfonate substituted groups. The maximum RE of all cationic and anionic dyes (RE > 90%) was achieved using EC‐Fe. The enmeshment of dyes on iron oxide/hydroxide precipitates and charge neutralization were the main removal mechanisms in EC‐Fe and EC‐Al processes, respectively. © 2012 American Institute of Chemical Engineers Environ Prog, 32: 547–556, 2013