The Pardoner is a hypocrite of sorts. His "duplicity," as stated by the host, shows the Pardoner to be a hypocrite. He preaches against what he practices. He openly boasts about his corrupt methods to extort money from gullible people. The relics that were "the pardons from the punishment due to sin" are sold by him rather than giving them to those who have done penance. He also sells "outrageously fake relics" in order to rip people off and make money. He brags how he dislikes humanity and prays on their guilt and stupidity.
In fact, the story that he tells parallels his character. His moral, "greed is the root of all evil," is told by personifying Avarice, Gluttony, and Sloth who meet their death at their own hands. These vices lead to their spiritual death much the same way as the Pardoner is spiritual dead because he enjoys these vices in life.
The Pardoner is characterized as an individual lacking moral scruples during the Prologue. As a member of the Roman Catholic church, he is expected to embody the tenets of this faith; however, the irony is established by the Pardoner's confession: he crafts fake relics in order to exact a pretty penny from the church congregation and pockets the indulgences that were meant to buy spiritual salvation. This is a flagrant disregard for the Christian teachings, since he is endorsing greed and dishonesty.
Important to note is the way in which the Pardoner is physically depicted. Being compared to a "gelding" or "mare" creates a unique characterization of the Pardoner. Gelding referred to a eunuch, who is a castrated, pre-pubescent male; this would explain the pardoner's high-pitched voice and lack of facial hair. The "mare" would be someone who was effeminate, potentially hermaphroditic or homosexual. In either interpretation, the Pardoner is crafted as aberrant sexually. This sexual deficiency would align with the Pardoner's moral deficiency, as it’s believed that the outward mirrored the soul. Therefore, through the physical depiction of the Pardoner, Chaucer furthers the base characterization of the Pardoner.
The actual tale indicts greed and jealousy; it reinforces Church teachings. However, the fact that the tale ends with the Pardoner trying to sell fakes after his confession indicates that the words of the Pardoner do not match his true self.