The Taiwanese government introduced a catch-and-report system for the whale shark Rhincodon typus in 2001, and in the following year limited the total allowable catch (TAC) to 80 individuals. This limit was reduced over the following years, reaching a low of 30 individuals in 2007. In November 2007, a comprehensive ban on R. typus fishing came into effect and protection measures were adopted for the species. This study measured and recorded the total length (LT), body mass and sex of 810 R. typus, using fisheries and other released data for the period 1995–2008. The mean LT of individuals caught from June to October was smaller than that for individuals caught from November to May. Mean annual catches in set nets were higher in south-western Taiwan than in other regions of Taiwan. The sex ratio showed that males were caught more frequently than females in Taiwanese waters, indicating sex segregation. For the first time, the stock structure, conservation and management regulation of R. typus in the north-west Pacific Ocean have been reviewed. The results provide a useful resource for future assessment of the possible development of R. typus ecotourism in Taiwan.