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This paper presents the detection of the equatorial plasma bubbles (EPB) using the Global Positioning System (GPS) ionospheric tomography method over Peninsular Malaysia. This paper aims to investigate the capability of the GPS ionospheric tomography method in detecting the variations of the EPB over the study area. In doing so, a previous case study during post-sunset 5th April 2011 has been selected as a reference for the detection of the EPBs over the study area. It has been observed that at least three structures of the EPBs have been captured based on the rate of change total electron content (TEC) index (ROTI) from 12 UT until 19 UT. Therefore, the three-dimensional ionospheric profiles have been reconstructed over Peninsular Malaysia using the tomography method during the study period in order to capture the signature of the EPBs. In this study, the detection of the EPBs using the tomography method is based on the rate of change of electron density (ROTNe). The results from three-dimensional ionospheric tomography show only two structures of EPBs are detected during the study period. It has been observed that the ROTNe depleted up to ~-12x109el/cm. Overall, the results in this study show that the GPS ionospheric tomography capable to be utilized in detecting the variations of EPBs in support of ionospheric studies and monitoring in the Malaysian region.