The church was dedicated, perhaps at the wish of the donor, Doge Jacopo Tiepolo, to the two brothers saints John and Paul (Zanipolo for the Venetians themselves) martyrs at Rome in the 4th century. The 13th century edifice was soon finished. But the importance of the church, immediately chosen as their burial place by many doges, and the rapidly spreading activity of the Dominican friars, made rebuilding necessary. At the beginning of the 14th century the construction of the majestic arcades began; the work was directed by the Dominicans fr. Benvenuto da Bologna and Nicolò da Imola. From 1333 to 1344 the Republic granted annual contributions; in 1343 stone, worked at the Doge’s Palace, was also granted. The works were interrupted in 1345 and resumed in 1355.
An inscription cut directly on the stonework of the last bay on the left, near the organ, records that in 1368 had; the nave and side aisles had been completed. In 1390 the procurators of St. Mark allocated 10,000 ducats from the bequest of Nicolò Lion «for building the said church of SS. John and Paul and the chapel of St. Domenico». This chapel was erected in 1395 on the spot where thee once stood – if it ever existed – the Oratory of St. Daniel, and where the Chapel of the Rosary now stands.
At the beginning of the 15th century a number of Venetian patricians were nominated Procurators of St. Zanipolo to ensure completion and continual embellishment. Finally, almost two centuries from its foundation, the church was consecrated on 14 November 1430 by the Dominican Antonio Correr, bishop of Ceneda, a Venetian noble and nephew of Pope Gregory XII.
In 1458, foundation of a College or Scuola to honour the Dominican saints Peter the Martyr of Verona, Vincenzo Ferreri and Cathe-rine of Siena. The Scuola of the Rosary was built in 1573 and in 1582 the chapel of St. Dominic was allotted to it.
After some six centuries (1806) the Dominicans are brutally ejected from their glorious home. The convent is turned first into a military, and then into a civil hospital.
In 1810, the parish of SS. John and Paul is created and entrusted to the surviving Dominicans.
During the night of 15-16 August 1867, fire destroyed the Chapel of the Rosary and with it 34 canvases including outstanding masterpieces.
At the beginning of the 20th century a complete restoration of the church was undertaken.
It was hit by bombs during the first world war, but fortunately nothing of importance was destroyed and this war-damage was quickly repaired; the work of restoration was finished in 1922.
The restoration of the Chapel of the Rosary was to take longer, it was concluded in October 1959.