The team was working on a £7m project to improve access between the city centre and the new Quays complex when the remains were unearthed on Tuesday.
The adult skeletons were uncovered, along with the remnants of a coffin, in the city’s Kimbrose Triangle.
They will not be displayed and will instead be given a respectful reburial after they are examined.
Nigel Edgeworth, manager for the Gloucester Linkages project, said: “We were putting in the foundations for a wall when we came across the two skeletons.
“The minute we go below half a metre we have an archaeologist watching us. It is very exciting from a historical point of view and adds more to the picture of Gloucester’s history.”