The dwarf stonebasher sibling species Pollimyrus castelnaui and P. marianne use differences in the electric organ discharges (EODs) for species recognition. As EOD waveforms are affected by water conductivity changes, the reliability of species recognition might be impeded due to natural variability in the environment. EODs of P. castelnaui (N = 8) and P. marianne (N = 8) under high (250 microS/cm) and low (25 microS/cm) conductivity were recorded and compared. Local peaks of the EODs of both species were significantly and predictably modified due to the conductivity change but species-specific differences were always recognizable. The duration of the EODs was not influenced by the conductivity change. Temperature alterations modified the duration in a linear relationship, allowing the determination of Q(10) values (1.6 for P. castelnaui's and 1.7 for P. marianne's EODs). As the species-specific differences are not masked by conductivity effects, EOD discrimination seems to be a reliable species recognition mechanism under natural circumstances.