Gymnotiform fish use their electric organ discharge for electrolocation and communication. They are active nocturnally and seek retreat sites during the day. We examined retreat site selection in Apteronotus leptorhynchus by assessing their preference for retreat tubes that differed in opacity and dimension. Isolated fish preferred opaque to clear tubes, long and narrow diameter tubes to short, wide diameter tubes, and open-ended to closed tubes. We also assessed how groups of fish distributed themselves in tubes according to sex and electric organ discharge frequency under four conditions: (1) unlimited tube availability, (2) limited tube availability, (3) variation in tube opacity, and (4) variation in tube dimension. When tube availability was unlimited, fish generally preferred to occupy tubes alone. However, females, but not males, often cohabited tubes with consexuals. When tube availability was limited, females were more often than males found outside of tubes. When tubes varied by opacity and dimension, fish clustered most commonly in preferred tube types (opaque and long tubes). Males with the highest electric organ discharge frequencies usually occupied the most preferred tube type. Thus, fish have clear preferences in selecting retreat sites and groups of fish reveal their dominance relationships when presented with variation in retreat sites.