The second reason for bioluminescence to be blue is that most organisms are sensitive only to blue light -- they lack the visual pigments which can absorb longer (yellow, red) or shorter (indigo, ultraviolet) wavelengths.

First, blue-green light (wavelength around 470 nm) transmits furthest in water. The reason that underwater photos usually look blue is because red light is quickly absorbed as you descend.

One special family of deep-sea fishes carries around its own "night vision" ability. This page explains how and why it uses this amazing adaptation.