Founded by E.P. (Pat) Bernuth and Capt. Jordan Monocandilos, Bernuth was conceived as a warehousing and stevedoring operation. Pat Bernuth was the owner of Bernuth Lembke, an international shipping and petroleum products conglomerate. In 1972, Capt. Jordan assumed the position of General Manager and Vice-President, overseeing the financial, operational, and marketing activities of the newly founded company, Bernuth Marine Shipping.

In 1974, Bernuth Lines, Ltd. was formed to serve the transportation needs of exporters to the Caribbean, Central America and the North Coast of South America. The m/v "Triumph" made its maiden voyage that year. Bernuth Agencies, Inc. became agents for the line in the United States. After E. P. Bernuth's death in 1977, Capt. Monocandilos became the sole owner of the company and guided its transition from a general cargo service to a scheduled container liner service, trading in the Eastern Caribbean and North Coast of South America. A pioneer in shipping, Bernuth claimed the honor of being the first liner service to directly call the ports of Isla Margarita, Nevis, Canouan and Mustique from the United States.

During the 1980s, Bernuth embarked on a vertical growth program which included the purchase of its Miami River terminal, container repair facilities, marine engine repair facilities, a trucking company, a tugboat company, an agency/stevedoring company in St. Maarten, Netherlands Antilles, and numerous vessels.

In May of 2001, Bernuth vessels began calling at Island Terminal, a private, deepwater terminal opposite the Port of Miami's Lummus Island. This marked a dramatic shift for Bernuth. A Miami River operator for nearly thirty years, at Island Terminal the Bernuth group gained the ability to employ newer, larger and faster ships to better service the needs of a growing customer base. Today, it enjoys the priviledged position of controlling its auxiliary services. As a result, Bernuth is widely regarded as the most flexible carrier in the trade.