Microbial indicators, the ratio of fecal coliforms (FC) to fecal streptococci (FS) and a newly defined enterococcus ratio, were used to differentiate pollution sources. FC FS values for municipal sewage were significantly higher than those values of the effluent from piggery wastewater. Enterococcus ratio, the ratio of (Enterococcus durans + E. hirae) to (Enterococcus faecalis + E. faecium), of human-sourced wastewater (0.90) was much lower than for pig-sourced wastewater (5.55). When FC/FS and enterococcus ratio were applied to a contaminated river study, both were corresponded well with the population density distribution of humans and pigs. FC/FS and enterococcus ratio are feasible microbial indicators for human- and pig-sourced wastewater pollution identification in field study.