The Lesser Adjutant (Leptoptilos javanicus) is a globally vulnerable stork species that is sporadically distributed in south and southeast Asia. In Malaysia, even though the population shows a gradual decline, the species population status in 2004-2006 is considered stable. However, the recent population status of the species is yet to be documented and is in question. Hence, we used data from the citizen science project, eBird to assess the population trend of Lesser Adjutants over 20 years in two selected sites in Muar, Johor. The population of Lesser Adjutants in Pantai Leka reduced over time while the population in Sungai Balang paddy field was likewise. The paddy field might become an alternate choice for the species due to developments and disturbances along the Pantai Leka shore. Most of the coastal mangrove forests in Muar have been degraded caused by the expansion of coconut and oil palm plantations; these remaining two valuable habitats need to be conserved. We discussed the population trends of Lesser Adjutant in two study sites and recommendations to conserve the species and its habitats.