This short communication presents a protocol for community amplicon sequencing on the Illumina HiSeq2000 and MiSeq platforms, which are known for their high-throughput and cost-effectiveness. The authors sequenced 24 microbial communities from various host-associated and free-living environments to validate the consistency of biological conclusions across different platforms. They found that the protocol successfully recaptured known biological results and that conclusions were consistent across the HiSeq2000 and MiSeq platforms, as well as across different regions of amplicons. The study demonstrates the suitability of these platforms for large-scale microbial community analysis, particularly in terms of reproducibility and cost-effectiveness. The results suggest that the reduced sequencing costs should be used to increase the number of samples rather than depth of sequencing for beta diversity studies. The protocol is expected to facilitate more widespread use of these platforms in microbial community research, contributing to the era of ubiquitous DNA sequencing.This short communication presents a protocol for community amplicon sequencing on the Illumina HiSeq2000 and MiSeq platforms, which are known for their high-throughput and cost-effectiveness. The authors sequenced 24 microbial communities from various host-associated and free-living environments to validate the consistency of biological conclusions across different platforms. They found that the protocol successfully recaptured known biological results and that conclusions were consistent across the HiSeq2000 and MiSeq platforms, as well as across different regions of amplicons. The study demonstrates the suitability of these platforms for large-scale microbial community analysis, particularly in terms of reproducibility and cost-effectiveness. The results suggest that the reduced sequencing costs should be used to increase the number of samples rather than depth of sequencing for beta diversity studies. The protocol is expected to facilitate more widespread use of these platforms in microbial community research, contributing to the era of ubiquitous DNA sequencing.