At the beginning of the first Matrix film, Agents track down Trinity at the derelict Heart O' The City Hotel, aided by the fact that Trinity had been conversing on a line that wasn't "clean" in spite of Cypher's assurances to the contrary. Although the Agents fail to capture Trinity, they conclude that
"The informant is real."
The choice of words clearly indicates that they did not know if an informant really existed, let alone the specific identity of the traitor in Morpheus' ranks.
How did they know prior to Trinity's Heart O' the City incident that Morpheus, or another Zion captain, may have had a traitor in his/her ranks? What made the Agents think that an informant willing to work with them may exist? Was it because Cypher initiated contact prior to the Heart O' The City incident and, if so, how did he do so without revealing his identity?