The Sea Organization or Sea Org is the senior-most status of staff within the Church of Scientology network of corporations, but is not itself incorporated. In the 1960s and 1970s, the Sea Org was started as L. Ron Hubbard's private navy, and adopted naval uniforms and ranks. Today, all Scientology management organizations are exclusively staffed with Sea Org members. The Sea Org maintains strict codes for its members, beginning with a billion-year pledge of service to Scientology upon initiation. David Miscavige, the leader of Scientology, is the highest-ranking Sea Org officer with the rank of captain. The higher rank of commodore is permanently reserved for the reincarnation of the late L. Ron Hubbard, founder of Scientology. Some ex-members and scholars have described the Sea Org as a totalitarian organization marked by intensive surveillance and lack of freedom.

In a 1992 memorandum by the Church of Scientology International, the following information was provided to the Internal Revenue Service with regards to the nature of the Sea Org:

[The Sea Org] does not have an ecclesiastical organizing board or command channels chart or secular existence such as an incorporated or unincorporated association. [...] Although there is no such "organization" as the Sea Organization, the term Sea Org has a colloquial usage which implies that there is. There are general recruitment posters and literature for "The Sea Org" which implies that people will be employed by the Sea Org when in reality they will join, making the billion year commitment, at some church that is staffed by Sea Org members and become employees of that church corporation. [...] The Sea Org exists as a spiritual commitment that is factually beyond the full understanding of the [Internal Revenue] Service or any other but a trained and audited Scientologist.

The Sea Org was established on August 12, 1967, by L. Ron Hubbard, the founder of Dianetics and Scientology, initially aboard three ships, the Avon River, the Enchanter, and HMS Royal Scotsman. Hubbard later rechristened the three vessels the Diana, the Athena, and the Apollo. The Apollo served as the flagship, or simply called "Flag", and Hubbard was referred to as Commodore.

In 1971, the Sea Org assumed responsibility for the delivery of the upper levels of its auditing and training, known as the Operating Thetan or "OT" levels. In 1981, under the aegis of the Commodore's Messenger Organization led by David Miscavige, Sea Org members dissolved the Guardian's Office (GO) and assumed full responsibility for the church's international management, later reassigning the GO's duties to the Office of Special Affairs in 1983 during the corporate restructuring of the Church.

It moved to land-based organizations in 1975, though maritime customs persist, with many members wearing naval-style uniforms and addressing both male and female officers as "sir". In 1985, the church purchased a 440-foot (130 m) motor vessel, the Freewinds, which docks in Curaçao in the southern Caribbean and is used as a religious retreat and training center, staffed entirely by Sea Org members. Sea Org members make a lifetime commitment to Scientology by signing a billion-year contract officially described as a symbolic pledge. In exchange, they are given free room and board, as well as a small weekly allowance. Sea Org members agree to strict codes of discipline, such as disavowing premarital sex, working long hours (on average at least 100 hours per week) and living in communal housing called berthing. They are allowed to marry, but must leave the Sea Org if they have or want to raise children.

According to Hubbard, much of the galaxy, including Earth (known as "Teegeeack"), was ruled tens of millions of years ago by the Galactic Confederacy. The confederacy was controlled by Xenu, a tyrant who was eventually overthrown by a group within the Galactic Confederacy known as the "Loyal Officers". Religious scholar Hugh Urban writes that the Sea Org is modeled after these Loyal Officers. Urban also describes the Sea Org, with the naval uniforms and ranks, as an idealized re-creation of Hubbard's own World War II military career. He says the Sea Org is reminiscent of the "Soldiers of Light" in Hubbard's science fiction story collection Ole Doc Methuselah. The publicized goal of the Sea Org is to "get ethics in on the planet".

Academic Stephen A. Kent has argued that at least part of the reason for the establishment of the Sea Org was that the Church of Scientology's practices encountered resistance from the American Food and Drug Administration and the Internal Revenue Service, as well as from the governments of the United Kingdom, Australia, and Rhodesia. Sailing on the high seas meant the church could escape their attention.