Mussels Mytilus galloprovincialis were collected monthly in 2 localities in the Northern Iberian Peninsula, Oia (Galicia) and Mundaka (Basque Coast), from April 2005 to May 2006, to investigate whether seasonal variability in biomarkers follows the same pattern at both geographical areas. The following battery of biomarkers was analysed: lysosomal membrane stability and structural changes, intracellular neutral lipid accumulation, cell type composition in the digestive gland epithelium, structural changes of digestive alveoli and digestive gland histopathology. Additionally, gonad index was measured as a supporting parameter. Overall, results demonstrate that most studied biomarkers showed similar seasonal variability pattern in both localities. Lysosomal membrane stability (labilisation period [LP]) and most histopathological conditions showed similar seasonal variability patterns in both localities, although values of LP and prevalences of some parasites were higher in Mundaka. Data provide baseline values to be used as reference values for the biomonitoring programmes carried out in coastal areas from Galicia to the Basque Coast. It is concluded that for monitoring programmes based on biomarkers, samples must be taken at least twice per year (spring and autumn) to avoid the effect on biomarkers of the late stages of each reproductive cycle.