A storm in 1842 destroyed the keeper's house and badly damaged the lighthouse tower.

The obsolete lamp and reflector system in the light was replaced by a Forward drop lens in 1856, which was more efficient.

[4] Congress appropriated funds for a replacement in 1874, but the Lighthouse Board stated, "This light can only serve a local commerce, of which, for several years, there has been little or none; and it is therefore recommended that the new work be indefinitely postponed."

In 1999, a team of maritime archaeologists led by Chuck Meide, as part of Florida State University's Dog Island Shipwreck Survey, discovered the remains of the Dog Island Lighthouse using side-scan sonar.

[5] The site was re-investigated by Florida State University archaeologists as part of a 2006 summer field school, and various features of the lighthouse—including remains of the keeper's house—were found.