This study aimed to clarify the effect of drought and the climate change phenomenon on the seedlings of seasonally dry tropical forests (SDTF). We collected data in a deciduous dipterocarp forest (DDF) and a lower montane forest (LMF) in northern Thailand. Seedlings were tagged, identified species, and recorded monthly from 2012 to 2018. ENSO index revealed that extreme El Niño happened between 2015 and 2016, resulting in less rainfall and a longer dry period than normal. The El Niño showed a negative effect on seedling mortality; massive seedling mortality occurred during the 2016 dry period, especially in LMF. The drought effect on mortality was significantly greater in evergreen than deciduous species. In contrast, the El Niño showed a positive effect on seedling recruitment in 2015 only in DDF. Massive recruitment was observed primarily in Quercus brandisiana (Fagaceae). After the El Niño, seedling density increased in DDF but decreased in LMF. The El Niño drought-affected seedling dynamics even in an Asian SDTF. The different effects of drought on seedlings of DDF and LMF suggest that future changes in the intensity of drought may alter the species abundance and distribution of seedling communities.