The partial and complete cycle of the intestinal pH-dependent oligopeptide transporter PepT1 from three species (seabass, zebrafish and rabbit) were studied using an electrophysiological approach and a biophysical analysis, in order to identify similarities and differences. On the whole the presteady state currents of the fish transporters were similar to each other, while presenting some quantitative differences with respect to rabbit PepT1: this last form showed slower decaying currents and the charge vs potential (Q/V) and time constant vs potential (t/V) curves shifted to more positive potentials All isoforms were similarly affected by external pH, showing acidity-induced slowing of the transients and positive shifts in the Q/V and t/V curves. Analysis of the pH dependence of the unidirectional rates of the intramembrane charge movement suggested that it is generated by the displacement of intrinsic charges of the proteins, and that external protonation of the protein limits the speed of this process. The complete cycle of the transporter was studied using the neutral dipeptide Gly-Gln. Michaelis-Menten analysis confirmed that in all species the apparent affinity for the substrate is significantly increased by acidity, while the maximal transport current is not strongly affected. Simulations using a kinetic model incorporating the new findings show good agreement with experimental data for all three species both with respect to the presteady-state and transport currents.