Will a 2001 Mazda 6 gearbox fit 1999 626?

The 2001 Mazda 6 gearbox may fit a 1999 626, but it is not a direct fit. The 626 has a Ford-based transmission, while the 6 has a Mazda-based transmission. You would likely need to modify the 6 gearbox to fit the 626. For these reasons, it is best to consult with a qualified mechanic to determine if the gearbox will fit and what modifications may be necessary.