The rats were widely diverse around the world. The identification of rat were difficult since most rats share common morphology characteristics. Thus, the identification through genetic material might help to identify the rat more accurately since the rat species were difficult to identify through the morphology characteristic. The aim of this study was to identify the unknown caught rats using phylogeny-based identification and further compared rat identification through morphological characteristics. Five rats’ samples were obtained from five different areas and the morphological characteristics of each sample were recorded to identify their species. The five rats’ tails were taken for DNA extractions by using high-salt method. The extracted DNA were amplified and sequenced for cytochrome oxidase 1 region. A total of 745 base pair were successfully sequenced for all samples and were aligned with 77 sequences retrieve from GenBank. Three phylogenetic trees were reconstructed Neighbor-Joining, Bayesian inferences and maximum likelihood method. Based on the morphological characteristics, the five samples were most likely identified as Rattus norgevicus for Rat 1, Rat 2 as Rattus tiomanicus, Rat 3 as Rattus andamanensis, Raat 4 as Rattus norvegicus and Rat 5 as Rattus exulans. However, further identification through phylogeny-based identification from the three phylogenetic tree shows that Rat 1 highly probably identified as Rattus norvegius, while Rat 2, Rat 3, Rat 4 and Rat 5 as Rattus kandianus and/or Rattus andamanensis
