The municipality of San Jose was formerly called "Ayuquitan", a name that was born due to a communication problem between the natives and Spanish Conquistadors. The story was that one day a group of Spaniards searching for flourishing communities came upon a group of natives harvesting rice. The Spaniards approached the natives and asked the name of the place while pointing to the ground filled with piles of rice chaffs. The natives thought they were asked for the name of the pile and answered "Inoquitan". From then on, the Spaniards called the place "Inoquitan". In time, the name "Ayuquitan" was adapted from the phrase "
may inoquitan". In 1902 Governor Demetrio Larena considered the place as a pueblo. Pioneer Spanish Merchant is Manuel Pastor. San Jose is the home of the old Spanish families settled since 1871 like the Patero, Amiscaray, Larena, Pareja, Siglos, Remollo, Renacia, Remata, Araco, Tatel and Remoto. San Jose was created as a town in 1954 from the barrios of Ayuquitan, Basak, Basiao, Cambaloctot, Calo, Cancawas, Hanay-Hanay, Jilocon, Lalaan, Naiba, Tapon Norte, Tampi, and sitios Guinsayawan, Kang-atid, Kangdajonog, Guilongsoran and Kaputihanan of the barrio of Siapo, all of which formerly belonged to the former municipality of Ayuquitan and then part of the municipality of
Amlan. ==Geography==