We evaluated three low frequency electrofishing pulse rates (30, 15, and 7.5 pulses per second [pps]) for differences in relative abundance, size structure and species composition of catfish species in two north Florida rivers (Apalachicola and Suwannee). Three species of catfish were collected from each river: Apalachicola River-flathead catfish (Pylodictis olivaris), channel catfish (Ictalurus punctatus), and blue catfish (I. furcatus); Suwannee River-spotted bullhead (Ameiurus serracanthus), channel catfish, and white catfish (I. catus). In both rivers, the dominant catfish species (Apalachicola: flathead catfish; Suwannee: spotted bullhead) was collected similarly with all three pulse rates. However, significant differences occurred in relative abundance, size structure, and species composition of the less dominant species in both systems. Generally, 15 pps yielded the best representation of sizes over the spectrum of lengths expected for all species; however 7.5 and 30 pps appeared to sample the smaller catfish (<260 mm) more effectively in the two systems studied. The use of 15 pps should give the best representation of catfish (>260 mm) while 7.5 pps will sample the smaller catfish (<260 mm) more effectively. Sampling with a combination of these pulse rates may be constructive when designing sampling strategies for standard sampling of catfish species.