Over one hundred years of vigorous progress in tropical cyclone (TC) research, the genesis of the cyclone (hereafter, tropical cyclogenesis) is remarkable as a doubtful subject. Furthermore, predicting tropical cyclogenesis, particularly in the lesser latitude, remains a significant challenge. Therefore, understanding the complex interactions in developing tropical cyclogenesis over the region is vital to improving tropical cyclogenesis forecasting. Hence, the Indonesia Maritime Continent is a tropical cyclone-free region due to decreasing the Coriolis effect. However, Seroja TC hits Flores (8.6o S, 120o E), east Nusa Tenggara, Indonesia, on 4 April 2021, and recorded as the first TC occurred over the mainland, which brought a catastrophic disaster in the region. This study investigated the tropical cyclogenesis of Seroja by using both observational and numerical studies. The results indicate that a marine heatwave and double vortices were favorable conditions produced preconditions to developing tropical cyclogenesis over the Maluku Sea. Thus, tropical cyclogenesis is formed by the breakdown of the intertropical convergence zone (ITCZ) associated with synoptic-scale wave train driven under the interaction of the Madden Julian oscillation (MJO) and equatorial Rossby waves. Moreover, our finding suggested that an extensive background cyclonic vorticity under the cold pool mechanisms is responsible for maintaining tropical cyclogenesis into a persistent Seroja TC.