The bulk of the Larkin Thorndike Lee papers consist of ships' papers documenting West Indian trading vessels which were mastered and/or owned by Larkin T. Lee of Beverly, Massachusetts. The collection also includes merchant correspondence, legal documents, personal, and estate papers. The collection is divided into two series.

Series I. Shipping Papers consists of ships' papers, merchant correspondence, and legal documents. The ships' papers contain the records of eight vessels which Lee mastered and/or owned from 1810 until 1827 (see Appendix I for a list of vessels owned). Miscellaneous ships' and shipping papers include accounts for unknown or multiple ships, as well as general business accounts with John Dike (1753-1837), Lee's attorney and possible business overseer. Merchant correspondence and legal documents contain market information, news of the disposition of goods, and a shop partnership agreement between Lee and Samuel P. Lovett.

Series II. Personal Papers consists of correspondence, financial, estate, and miscellaneous papers. Although the bulk of the personal papers contain household bills and receipts, they also feature correspondence regarding a mummy which Lee helped to import to the United States in 1824. The estate papers include an inventory of Lee's estate, as well as correspondence with his widow and legal documents. Miscellaneous papers include a deed of Larkin T. Lee, Jr.