Operational taxonomic unit (OTU, defined at 97% sequence identity) richness and evenness of the digestive microbiota were investigated for each algal treatment and sampling date. When all sampling dates were pooled, alpha-diversity did not significantly vary between algal diets on average, but when algal diets were considered separately, alpha-diversity followed different seasonal patterns. In the case of the L. digitata diet, samples from colder months (February–April 2012, January 2013) presented significantly lower alpha-diversity indices on average than those from warmer months (Wilcoxon test, P < 0.001, Additional file 1: Figure S1, Additional file 2: Table S1). In the case of the S. latissima and U. lactuca diets, diversity increased over the year and diversity seemed stable with time for the P. palmata treatment.