Next generation sequencing (NGS) is a widely accepted technology used by microbial ecologists for metagenomic analysis of complex microbial communities. As technologies continue to improve, it is necessary to compare data sets obtained from different platforms and analyze their effect on community structure. In the present study, we compared the 454 data set with that of Ion Torrent Personal Genome Machine (PGM) on the same DNA samples (n = 14) obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in number of reads and length of reads, the platforms provided a similar community structure. The weighted UniFrac distances between the samples that were sequenced on both 454 and PGM were significantly correlated, as determined by Procrustes analysis of principal coordinate matrices (M2 = 0.319; Monte Carlo P < 0.001). Though similar major abundant phyla were detected by both platforms, PGM recovered 4 additional phyla. At the genus level, there was no substantial variation between the 454 and PGM data sets for each animal except for Prevotella, Cyanobacteria YS2 and Succiniliclasticum (P < 0.05; chi-squared test). However, there was variation in the abundance of genera between different animals, irrespective of the platform used. Collectively, the present study will be useful for microbiologists/ecologists to compare the microbial community structure obtained from different platforms; particularly with the expectation 454 will be completely replaced by PGM and/ or Illumina.