Prokaryotes exhibiting different environmental characteristics show different extents of codon usage bias. The 518 prokaryotes were classified according to various properties, and the distributions of CAIave values of the different classes were compared. (a) Pathogenic prokaryotes show larger extents of codon usage bias than non-pathogenic prokaryotes. CAIave is indicated as 'Average CAI'. (b) Facultative prokaryotes show the largest extent of codon usage bias and anaerobic prokaryotes show the smallest extent. (c) Prokaryotes that live in different salinity environments show a statistically significant difference in CAIave values. (d) Thermophilic and hyperthermophilic prokaryotes show a smaller extent of codon usage bias than mesophilic prokaryotes. CAI: Codon Adaptation Index; GC: genome content.