The first part of the line is a reference to the Denial of Peter: on three occasions Jesus's disciple Peter denied knowledge of him. It appears in all four gospels of the New Testament, for example in Matthew 26:34 (King James Version):
Jesus said unto him, Verily I say unto thee, That this night, before the cock crow, thou shalt deny me thrice.
The second part of the line refers to the Kiss of Judas, the kiss given to Jesus by his disciple Judas Iscariot in the Garden of Gethsemane in order to identify him to the Roman soldiers, an event sometimes known as the Betrayal of Christ. In Mark 14:44-45 (King James Version), it is recounted thus:
And he that betrayed him had given them a token, saying whomsoever I shall kiss, that same is he; take him and lead him away safely./And as soon as he was come, he goeth straightaway to him and saith, Master, master, and kissed him.
Used figuratively, a kiss of Judas may refer to any act which appears on the surface as an act of friendship but is in fact an act of betrayal or malice.