Santa Cruz das Flores (Portuguese pronunciation: [ˈsɐ̃tɐ ˈkɾuʒ ðɐʃ ˈfloɾɨʃ]) is a municipality situated in the north half of the island of Flores, in the Portuguese archipelago of the Azores. Situated in the sparsely populated Western Group, the population in 2011 was 2,289 inhabitants in an area that covers approximately 70.91 square kilometres (27.38 sq mi), bordering the southern municipality of Lajes das Flores.

The earliest record of the northern municipality referred to the village of Santa Cruz das Flores, in 1548. Transcribing the works of Father [Gaspar Frutuoso], Francisco Gomes documented the arrival of the crew of the nau Nossa Senhor da Misericórida. He included Gaspar Frutuoso's 1589 reference, described the growing urban area of Santa Cruz as a "well divided and plane villa" covered in thatched roofs. Ponta Delgada, he continued, was a parish of 30 neighbours surrounding its small hermitage (dedicated to Santo Amaro, even as its ecclesiastical patron since the 16th century was the apostle Peter).

In the beginning of the 17th-Century Diogo das Chagas, referred to the villa of Santa Cruz as the "head of the island" and the center of the administration, noting "[the village]...is very well located with the best port on the island...". He described his hometown as built on "firm foundations", delimited by its interlocking roads that began at the Santa Cruz sandbar and the other the port of Poças, all in the direction of Monte Calvário (today, Monte das Cruzes). He described "...the first road of the village and from the Porto das Poças another road, which is the last in the village, and where the rest of the roads intersect...". This year marked the municipal administration of the northern half of the island; part of the administrative regalia, was the obligatory construction of a lighthouse.

A primitive church, dating to the 16th century and constructed in 1627, by vicar Inácio Coelho, who in 1641 also provided land for the founding of the Franciscan Convent of São Boaventura, as well as the bread and wine for religious ceremonies.

By the end of 1693, Friar Agostinho de Mont'Alverne, referred to 9000 inhabitants, living in 180 homes, primarily in the village of Santa Cruz. These original settlers were Portuguese, primarily from the area of the Alentejo and Minho. It was about this time that the third oldest of the parishes was created by the Diocese in Angra, on 9 July 1693: Nossa Senhora do Pilar, delimited by the ravines of Barrosas (in the north) and Alagoa (in the south). The two localities that formed the parish, Cedros and Ponta Ruiva, de-annexed from the parishes of São Pedro de Ponta Delgada and the Matriz de Nossa Senhora da Conceição, in Santa Cruz, included 50 homes and 176 people. With its presbytery and image of it patron saint provided by the Count of Santa Cruz, its primitive parochial church was later expanded in 1719 and reconstructed in 1822.

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