[3] The project is led by Dan Whaley, co-founder of GetThere, one of the first online travel booking systems in 1995.

[3][8][9] Its advisors have included John Perry Barlow, Charles Bazerman, Philip Bourne and Brewster Kahle.

[2] A Kickstarter drive to raise $100,000 to fund a working prototype narrowly reached its goal on November 13, 2011.

[17] In December 2015, Hypothes.is was a founding member of a coalition of scholarly publishers, platforms, libraries, and technology organizations to create an open, interoperable annotation layer over their content.

[18] In August 2022, after noting that being a nonprofit limited the company to grants and donations and with several of the key funding sources Hypothes.is relied on no longer available, they formed "Annotation Unlimited, PBC" (Anno).