Beginning in 1879, Harvard graduate Alpheus Hyatt along with his assistant Balfour van Vleck began running a summer school in Woods Hole. Woods Hole at the time was a small village located at southwest tip of Cape Cod, and was home to a guano factory that employed a few hundred people from the surrounding countryside. In the mid-1880s the guano factory went out of business, resulting in an economic recession in Woods Hole, but had the nice byproduct of making the air more enjoyable again. As a consequence, Woods Hole became an attractive location for wealthy people who could vacation by the sea while taking advantage of the relatively cheap labor to help in their households. Given this economic context, and due to the variety of ponds and lagoons and its rich and complex bays, Woods Hole seemed to be the most suitable place for scientists to study marine life by the sea. With the help of Spencer Fullerton Baird, who at the time directed the US Fish Commission also located in Woods Hole, Hyatt managed to secure some lands, which were eventually used to build the first wooden building of the MBL. On March 20 1888, with a starting budget of $ 10,000, the Marine Biological Laboratory was incorporated with a board of trustees that included Hyatt.
The money that had been raised to start the MBL was a great achievement at the time, but was not enough to cover salaries. However, before summer came, the board of trustees was determined to hire a director for the MBL. First, they sent out an invitation for directorship to Samuel Clarke, who worked at the Williams College. Given the implications of running an institution pro bono, including having to cover his living and travel expenses in addition to the amount of labor that a directorship implies, Clarke rejected the offer. Next, the board of trustees offered the directorship of the MBL to William Brooks at Johns Hopkins University, hoping he could come and bring the support of his primary institution. After some time, Brooks turned down the offer.
Finally, the board of trustees invited Whitman to direct the MBL. Similar to the other candidates who had been identified for the role, Whitman represented an ideal director in many respects, including the fact that he had previously directed another biological laboratory, namely the Allis Lake Laboratory in Wisconsin. Almost immediately and with great enthusiasm, Whitman accepted the offer and he served as the MBL director from 1888 to 1908. During his directorship, Whitman managed to gather funding to sustain the MBL and to pay not only for the facilities maintenance and research supplies, but also for lecturers to teach summer courses. Throughout his career as the MBL director, Whitman kept the independence of the MBL as a non-negotiable priority as well as an inspirational value.