Charged amino acids (AAs) are targets for selective forces in protein evolution. To fully explore the trend of charged AA frequencies evolution in macroevolutionary process from prokaryotes to eukaryotes, we extend the analysis of five charged AAs separately and total basic and acidic AAs in protein sequences of 158 prokaryotic and 63 eukaryotic predicted proteomes and 456 clusters of orthologous groups (COGs). Also, we eliminate the biases that may caused by extreme organisms in both predicted proteomes and COGs analyses. More basic AAs, His,Lysand Glu were found in eukaryotic proteins compared with prokaryotic proteins by predicted proteomes analysis. By COGs analysis, we found that basic AAs andLysfrequencies are higher in eukaryotic orthologous proteins than their prokaryotic companions, while the trend of Arg frequency is the opposite. We discussed the agreements and disagreements of two analyses and gained a more credible trend of charged AAs evolution in macroevolutionary time scale.