The　microbial　community　in　endogenous　denitrification　and　denitrifying　phosphorus　removal　treatment　at　transcription　level　was　unknown.　This　study　first　confirmed　the　expression　of　actually　active　bacteria　in　endogenous　denitrification　and　denitrifying　phosphorus　removal　system　to　treat　low　C/N　municipal　wastewater.　No　external　carbon　source　was　added　to　influent　wastewater.　The　cDNA　high　throughput　sequencing　showed　that　Candidatus　Accumulibacter　was　the　most　effective　polyphosphate　accumulating　organisms　(PAOs)　that　actually　worked　rather　than　Dechloromonas,　which　was　different　from　the　result　at　gene　level.　Reverse　transcriptional　PCR　(RT-PCR)　and　analysis　of　Variance　(ANOVA)　suggested　that　the　ratios　of　dead　or　dormant　bacteria　could　monitor　wastewater　treatment　process.　Identification　of　active　microbial　community　at　transcription　level　demonstrated　that　the　synergy　of　endogenous　denitrification　by　glycogen　accumulating　organisms　(GAOs)　and　denitrifying　phosphorus　removal　by　Candidatus　Accumulibacter　fully　utilized　the　internal　carbon　source,　and　effectively　solved　the　problem　of　carbon　source　deficiency　in　municipal　wastewater　treatment.