HBOI is comprised of seven divisions that include: Aquaculture; Biomedical Marine Research; Engineering R&D; Environmental Laboratory; Marine Operations; Marine Science and Marine Mammal Research and Conservation.

To carry out its work, HBOI has designed, built and outfitted the world's most technologically advanced fleet of ocean going research vessels and submersibles. This gives HBOI a unique combination of specialized capabilities, allowing for the exploration of almost every aspect of the world's oceans.

Harbor Branch Oceanographic Institution is located along the Indian River Lagoon in Fort Pierce, Florida. The 600-acre campus is home to dozens of premiere research and development facilities. HBOI employs over 250 scientists, technicians, and engineers, many of whom are leaders in their fields. HBOI is one of the few organizations capable of planning and executing research operations, building the necessary instrumentation, taking it to the ocean depths anywhere on Earth in submersibles of its own design and construction, analyzing findings in its own labs, and finally sharing this hard-won knowledge with the world.

First submersible was HBOI's present JOHNSON-SEA-LINK I (JSL I), developed by Edwin Link in the late 1960's with financial support from Seward Johnson. Early JSL activities were centered around "lockout diving" wherein a diver would leave the rear compartment (the "dive chamber") to conduct underwater operations. (Lockout diving was discontinued in the late 1980's). JSL I was commissioned on January 29, 1971. Its twin, JSL II, was commissioned in December 1975.

First research vessel was the R/V GOSNOLD, a surface operations ship owned by Woods Hole Oceanographic Institution until its sale to Harbor Branch. GOSNOLD missions trawled, dredged and boxcored for five years, forming the basis of the research collections now housed in the Harbor Branch Oceanographic Museum.