Clam Ruditapes decussates was used as a biomonitoring organism to measure the potential impact of pollution. The present study investigated histological alterations of R. decussates following a long-term exposure to a sublethal-level of pesticides Reldan and Roundup. The clams were taken to the laboratory and kept for days to adjust to a continuous closed flow system with quality water control. After the adjustment period, clams were exposed either to sublethal concentrations of Reldan (0.6 µl L − 1 ) or Roundup (1.1 µl L − 1 ) for 90 days. Clams were taken to determine the histological damage at 30, 60 and 90 days. Most histological alterations were highly localized in the glandular cells of the gills, mantle tissues and digestive gland; secretions of glandular cells were found to be increased by increasing the time of exposure. Histopathological results showed the activation of resistance mechanisms that allowed the clams to survive under sublethal stresses. Thus, histological changes on localized tissues were sensitive and they have positive correlation to the time of exposure to the pesticides, suggesting that they may serve as biomarkers for Reldan and Roundup exposures.