The effect of cellulase treated rice straw on the molecular diversity of rumen bacteria in Philippine native cattle was investigated. A 3×3 Latin Square Design (LSD) was used to evaluate the effect of cellulase supplementation on the rumen bacterial diversity of Philippine native cattle fed rice straw. Three different treatments consisted of Treatment 1: urea-molasses-treated rice straw (UMTRS); Treatment 2: cellulase mixed with urea-molasses pre-treated rice straw (UMCTRS) and Treatment 3: Cellulase treated rice straw (CTRS). Changes in rumen bacterial diversity due to the dietary treatments were determined by Polymerase Chain Reaction – Denaturing Gradient Gell Electrophoresis (PCR- DGGE). The DGGE was used to separate PCR product of the amplified 16S rDNA or its regions. The sequence analysis of purified PCR product amplified from excised DGGE bands was used to determine the phylogenetic placement of each individual band in the community. Results of DNA sequencing showed the presence of more amplicons in UMCTRS and CTRS indicating that these treatments led to increase in the population of fibrolytic microorganisms in the rumen. Results of an in situ study also showed that these two treatments have ability to improve feeding value. We concluded that cellulase has a positive effect on feeding value of rice straw especially with the addition of cellulase to urea-molasses pre-treated rice straw.