While both are derived from blue-green algae, the biggest difference between green spirulina and blue spirulina is that green spirulina is the whole food, while blue spirulina is an extract of the phycocyanin from the green.  Some of the more practical differences are that green spirulina has a super strong fishy smell and taste, while blue is fairly mild.  Also, blue spirulina has quite a bit more nutrients packed into it than green.