In all pueblo societies, language has a direct connection to religion. Language is a fluid and ever-evolving medium with a spirit of its own. The story of prehistoric history in the Southwest has to include the migration of clans and ritual specialists, each with terminology of their own. All the pueblos are also congregations of different clans.
In several cases, it wasn't until it became clear to tribal elders that their language was dying before they would allow the creation of a written version or a dictionary of their language as part of the efforts to preserve their language(s). The people of Jemez still forbid any written forms of their language and that stops development of a Towa Dictionary... and the people of Jemez are the only speakers of Towa (Pecos Pueblo also spoke Towa but when that pueblo was abandoned in the early 1800's, the people of Pecos were invited to move to Jemez and they did so. They do still return to the site of Pecos Pueblo every year for certain religious ceremonies).
Native languages spoken among the pueblos are Hopi, Zuni, Keres, Tiwa, Tewa and Towa. Many Hopi and Hopi-Tewa also speak Navajo. There are still a few in the Southwest who have never learned to speak English.
Zuni has been classed as a complete "isolate" (meaning: isolated so long it has developed along its own path without traceable root). However, when it comes to religion, the Zuni share many words with the Hopi, the Keresans and the Pimas (from down south in Arizona).
Keres is also classed as an isolate and the two main branches, Eastern and Western, are sometimes classed as separate languages. However, many words around religion, kiva practices and clan societies are shared with Hopi, Zuni and all the Rio Grande pueblos.
Hopi is classed as a member of the Uto-Aztecan family, a group of languages that span from central Mexico to Oregon and Idaho. Hopi as a language varies depending on which village we're talking about. The Hopi spoken at Walpi has significantly more words of Tewa, Towa and Keres derivation than the Hopi spoken at Oraibi. And then there's Sichomovi, the Zuni pueblo on 2nd Mesa. It's not just a matter of dialects either.
Tiwa, Tewa and Towa have been grouped in the Tanoan-Kiowa family of languages. In the Tanoan-Kiowa group, Towa is closer to Kiowa than to Tewa-Tiwa but all tongues in the group share a common ancestor. A proposal has been put forth that would convert the Tanoan-Kiowa family to a Tanoan-Aztecan family with a connection to the Uto-Aztecan family and the greater overview that would create would potentially bring the Zuni language into connection with that proto-language.