A mesoscale data assimilation (DA) system was developed for low latitudes, and DA experiments for the tropical cyclone Nargis were conducted. A tropical cyclone bogus (TCB) procedure was developed for the Bay of Bengal, and the impact was investigated.The Meso 4D-Var system of the Japan Meteorological Agency (JMA), which was designed for operational mesoscale DA in the mid-latitudes, was modified for DA application in the tropics. Since the relationship of the geostrophic wind was not available near the equator, a weighting function for the regression coefficient matrix for the unbalanced wind was determined based on statistics. Six DA experiments were performed to produce the initial field at 1200 UTC on April 30, 2008, in order to assess the impact of the DA periods (12 h and 24 h) and two different TCBs. Analyzed initial fields were compared with the JMA global analysis (GANAL), the best track data of RSMC, New Delhi, and the cyclone track estimation of the Indian National Centre for Ocean Information Services (INCOIS). Precipitable water vapor (PWV) around the cyclone was less than 65 mm in GANAL; in DA analyses, areas with more than 60-mm PWV were more widespread, especially to the east of the cyclone, and the maximum values exceeded 70 mm near the cyclone center. The cyclone center position was also improved by DA and the implementation of TCB; however, the cyclonic circulation was underestimated in the 24-h DA without TCB (MA24). Lack of satellite observations of the Bay of Bengal in the first 12-h assimilation windows was determined to be the reason for this underestimation. Mesoscale numerical predictions using initial fields produced by Meso 4D-Var were conducted, and the results were compared with the prediction using GANAL (control run; GA). Overestimation of the cyclone speed and the resultant positional lag in the control run were ameliorated by modifying the initial field by DA. Differences between the upper flow in the GA analysis and that in DA analyses might account for the difference in cyclone speed. Cyclone development was well predicted except in the MA24 experiment, in which underestimation of cyclonic circulation at the initial time caused subsequent insufficient development. Northward biases were observed in several predicted cyclone tracks. Differences between precipitation in the MA24 and that in other experiments might be one of the reasons for the differences in cyclone track.