We use two taxonomic indexes to assess the variability of the taxonomic structure and diversity of the ichthyofauna of two low-energy environments in southern Brazil and to compare the temporal patterns of these two ichthyofaunas. Sampling was conducted in the infralittoral zones of Maciel (Paranaguá Bay, PR) and Indio Beach (Norte Bay of Florianópolis, SC). A fyke net was set up at a depth of 0.5 to 2.0 m and left in place for 48 h for each of the samplings. A total of two diurnal and two nocturnal samplings were conducted monthly per one year. The ichthyofaunas at the two sites exhibited similar temporal dynamics, with their abundance and biomass presenting a tendency to increase with increasing temperature during the spring and summer months. A total of 113 species were captured, of which 47 were present at both sites. Harengula clupeola, Sphoeroides testudineus and S. greeleyi were especially abundant at both sites. The co-occurring species displayed similar day and night occupancy trends. In all seasons, the obtained values for the average taxonomic distinctness and variation in taxonomic distinctness were within the confidence intervals. The seasonal reproduction and recruitment patterns led to slight changes in taxonomic distinctness during the year, which were within the expected intervals.