2199 was the Real World year (as assumed by Zion) when Neo was extracted from the Matrix. As Morpheus explained to the newly freed Neo, the figure "2199" was just an approximation and that no one from the Resistance was certain what year it actually was.
However, as The Architect later revealed to Neo during his explanation of The One's part as the bearer of the Prime Program, the Resistance were being deceived and there were already five previous iterations of both The One and Zion. The Architect also explained that once every century, the current Zion was destroyed and The One would need to sacrifice himself to reload the Matrix, resulting in the memories of all Bluepills being presumably erased during the reload. And while the destruction of Zion meant the annihilation of all current Zionites, The One was allowed to select twenty-three individuals from the Matrix to rebuild a new Zion.
This pattern guaranteed that, besides the Machines, no one could have kept an accurate record of time. This also explained why, while Morpheus thought that the current year was 2199, it could have actually been as late as 2699 (assuming that each iteration of the previous five Zions lasted at least 100 years) or even later still.