In recent years, climate changes accompanied by unstable water quality have often caused outbreaks of diseases, followed by mass mortality of farmed tilapia in Taiwan. Francisellosis was previously known as piscirickettsiosis (rickettsia-like organism infection), but now the pathogens involved have been renamed to Francisella spp. The disease has been reported as occurring in different countries in Europe, North and South America, and Asia (including Taiwan), causing infections among a variety of wild fish and farmed fish, and resulting in serious economic losses to the aquaculture industry. This paper investigated the francisellosis infections of farmed tilapia in Taoyuan and Hsinchu areas during different seasons, considering clinical signs and the relation of water transmission from 2009 to 2011. The results showed that Francisella spp. found in Taoyuan and Hsinchu areas cannot be isolated on common artificial media. The pathogen can be identified as F. noatunensis subsp. orientalis by polymerase chain reaction and DNA sequence assay. Downstream pools may be infected by water transmission from the drainage of upstream farms. There are two peak periods for francisellosis outbreaks, March-April and October-November, due to these periods are the most suitable temperature for the reproduction of F. noatunensis subsp. orientalis.