Sunfishes (Molidae) comprise the largest bony fishes inhabiting tropical and temperate ocean regions. Though they occupy both epipelagic and mesopelagic realms, they are principally non-targeted bycatch species and are captured by longline, harpoon, drift net, and set net fisheries in eastern Taiwan. Due to increasing numbers of removals from the fishery, there are concerns how this trend may affect the population dynamics and facilitate the possible decline of the stock. Complicating the situation for management is that the ecology and population dynamics are poorly understood for this species and whether current exploitation levels are sustainable. To fill in some of the necessary gaps in knowledge of sunfishes for local fisheries management, we investigated variability in species composition, abundance, size composition, and the possible correlation with sea surface temperature (SST) in eastern Taiwan. Fishery data of sunfish was collected from Shingang fish market, Taitung, from January 2016 to October 2017, and from the set-net complex, Hualien, from January 2003 to December 2011. The species comprised Masturus lanceolatus (80%) followed by Mola spp. (20%). Species abundance, average standard length, and size composition exhibited seasonal variability and abundance reached a peak in winter when SST was low (21°C). Small, immature individuals first appeared in winter and then sharply decreased in summer and the proportions of the largest individuals were highest in summer. The stock abundance of Masturus lanceolatus was highest in winter and late spring/early summer with recruits entering the fishery off eastern Taiwan. Variability in population dynamics appeared to be closely associated with water temperature, their life history traits and behavior.