The size of the sieve mesh opening use to hold the benthic macrofauna could affect certain biotic indicators utilized to describe the ecological status of a given benthic system. The objective of this study was to determine the effect that the lower limit of the mesh opening could have in the estimation of species richness, Shannon-Wiener diversity index and AZTI marine biotic index (AMBI). Data was collected from sediment samples obtain in stations located in and out (reference) of two mussel farms from Reloncaví Sound. The samples were sieved through two sizes of mesh opening: 1 mm and 500 µm. The benthic macrofauna was identified and quantified as ≥500 µm and ≥1 mm. The AMBI, Shannon-Wiener diversity index (log2) and species richness was estimated. Indicators estimated from information obtained with the ≥500 µm and ≥1 mm mesh were compared through a t test. The most abundant species on both localities was the polychaete Chaetozone setosa, assigned to the ecological group GE IV, and the Ostracoda Class, assigned for Chilean experts to the ecological GE 2. Significant differences were observed only in species richness at stations within the culture (in the Center 2). According to the estimated biological indicators the ecological status of benthic systems under the farms is acceptable based on the limits established for diversity and AMBI. Using a mesh size of 500 µm results in larger abundances of opportunistic species, but this change had no effect on the classification of the ecological status of the benthic system.