Ciprofloxacin and sulfamethoxazole are two antibiotics commonly detected in the aquatic environment, but information on their toxicity towards natural microbial communities is largely absent. In particular no data are available for marine microorganisms. Aim of the current study was therefore to evaluate the chronic toxicity of ciprofloxacin and sulfamethoxazole on natural marine biofilms (periphyton), a complex ecological community comprising a variety of bacterial and algal species. The biofilms were sampled along the Swedish west coast and subsequently exposed over 4 days in a semi-static system to a concentration series of each antibiotic. Effects on the bacterial part of the periphyton community were assessed using Biolog Ecoplates, reflecting total respiration and functional diversity of the bacterial community. Exposure to either antibiotic resulted in a clear concentration-response relationship with EC10 and EC50 values for the inhibition of total carbon source utilization of 46.1 nmol/L and 490.7 nmol/L for ciprofloxacin, respectively 56 and 1073 nmol/L for sulfamethoxazole. The NOEC for ciprofloxacin was 26 nmol/L, with a minimum significant difference of 19.24%, for sulfamethoxazole it was 140 nmol/L with a minimum significant difference of 14%. Multivariate data exploration of the whole carbon source utilization pattern confirmed these results. The data indicate that sulfamethoxazole leads to a general decrease in carbon source utilization, while ciprofloxacin exposure leads to a re-arrangement of the carbon-utilization pattern in the region of 20-50% effect. This corresponds with the higher specificity of ciprofloxacin for certain bacterial species. Effects on the algal part of the communities were evaluated by analyzing the amount and composition of photosynthetic pigments, and neither ciprofloxacin nor sulfamethoxazole caused any inhibitory effects up to the maximum tested concentration of 9 000 nmol/L. However, sulfamethoxazole exposure did lead to a significant stimulation (75% above control level) of the total pigment content of the biofilm already at the lowest tested concentration of 5 nmol/L. The stimulation then decreased with increasing concentrations to finally return to control level at 3 000 nmol/L. No shifts in the relative pigment composition were observed, indicating a generally increased algal biomass without major shifts in community composition.