The Civic Historical Archive also holds a collection of manuscripts of Genoese history, formed between the late 19th and early 20th century through purchases and donations.

The oldest group dates back to 1882, when the City acquired 81 manuscripts from the library of G. Ambrogio Molfino, including some unique pieces of great value.

The manuscript which made the Molfino Collection famous is the Anonimo Genovese, a 14th-century parchment codex by an unknown author containing poems in Genoese and Latin verse.

Another highly valuable item is the Memorie della città di Genova e di tutto il suo Dominio (Memories of the City of Genoa and its Domain) by Giovanni Battista Cicala, Genoese nobleman, Senator and Governor of Corsica in 1651. The work, in six large volumes, consists of the painstaking collection of all the news known by the author concerning the events of Genoa, schematically annotated and in chronological order, from the legendary city's founding to the year 1528.

Also of great interest in the Molfino Collection are various manuscripts of ecclesiastical history, including the 17th-century Diario Sacro e Curioso per Sapere le Feste sì della Chiesa come di Genova (Holy Diary of Feast Days in the Church), almost all the works of Giscardi, including Origine e successi delle Chiese, Monasterii e Luoghi pii della Città e Riviere di Genova (Origin and successes of the Churches, Monasteries and Sacred places of the City and Riviera of Genoa), Inscrizioni et Epitafii ne luoghi sacri e profani della Città e Dominio di Genova (Inscriptions and Epitaphs in sacred and profane places in the City and Domain of Genoa), and the Alberi di più Famiglie Genovesi (Genoese Family Trees). Not forgetting the collection of 150 letters from Cardinal Mazarino to Marquis Giannettino Giustiniani of Genoa, some handwritten, others signed or with additions in his hand.

In 1866 a group of manuscripts was acquired from the superb library owned at the end of the 16th century by Genoese nobleman Giulio Pallavicino, a historian and man of letters known principally for being one of the founders of the “Accademia degli Addormentati”.

The collection, known as the Pallavicino Collection, consists of a vast quantity of volumes, written almost entirely in his own hand, containing copies of laws and decrees, lists of consuls, elders, senators, and members of the Councils of the Republic, collections of instructions for ambassadors and their reports, news about Genoese families, and miscellaneous documents.

Also noteworthy in the same collection are the Vero e distinto ragionamento ... per lo quale con ogni curiosità si narra la scellerata guerra mossa l’anno 1625 dal Duca di Savoia alla Repubblica di Genova (True and clear account... which tells every detail of the heinous war of the year 1625 waged by the Duke of Savoy on the Republic of Genoa), an original work by Pallavicino, the Inventione di Giulio Pallavicino di scriver tutte le cose accadute alli tempi suoi (Idea of Giulio Pallavicino of writing all the events of his time), a juvenile diary from the years 1583-1589, and a paper manuscript of the early 16th century, known as the Miscellanea Umanistica, containing passages by classical authors.

In 1892 the Archive's manuscript collection grew with the addition of another hundred manuscripts thanks to Bequest Giovanni Ricci. This collection included various volumes of Leggi e Decreti della Repubblica di Genova (Laws and Decrees of the Republic of Genoa), a set of the most famous local chroniclers and historians, works of ecclesiastical history, reports from ambassadors, and instructions from courts to ministers.

Also of note, a copy of the Stato presente della Metropolitana di Genova (Present state of the City of Genoa) by F. M. Accinelli, with detailed maps of the various parishes of the city (18th century), a 16th-century copy of the Annals by Antonio Gallo, some beautifully-bound volumes from the 18th century, including two volumes of Capitoli delle arti degli Osti e Tavernari (Chapters on the arts of Hosts and Taverners), and the Historia della guerra fra Papa Paolo IV e Filippo II re di Spagna (History of the war between Pope Paul IV and Philip II King of Spain) by Pietro De Nores, of the 17th century.

The manuscript collection continued to receive sporadic additions through donations and purchases in the late 19th and early 20th century.  Among these stand out  the statutes of the venerable « Compagnia del Mandiletto », a charitable organisation established in Genoa in 1497, and the Histoire Générale de la Revolution de Gênes contenant tout ce qui s’est passé dans cette république depuis la mort de Charles VI, jusque a’ la levée du siège, par les Allemans by Ange Goudar.