Morpheus and his crew are a group of rebels who hack into the Matrix to "unplug" enslaved humans and recruit them; their understanding of the Matrix's simulated nature allows them to bend its physical laws. Morpheus warns Neo that death within the Matrix kills the physical body too and explains that the Agents are sentient programs that eliminate threats to the system, while machines called Sentinels eliminate rebels in the real world. Neo's prowess during virtual training cements Morpheus's belief that Neo is "the One", a human prophesied to free humankind. The group enters the Matrix to visit the Oracle, a prophet-like program who predicted that the One would emerge. She implies to Neo that he is not the One and warns that he will have to choose between Morpheus's life and his own. Before they can leave the Matrix, Agents and police ambush the group, tipped off by Cypher, a disgruntled crew member who has betrayed Morpheus in exchange for a deal to be plugged back into the Matrix to live a comfortable life.
What are agents in the matrix and what is their relationship to sentinels?
Agents in the Matrix are sentient 'programs' designed to remove threats from the system. They can be thought of as an Anti-Virus solution within the Matrix program. 

Sentinels are physical squid-like robots in the real world outside the matrix whose aim is to destroy and capture remaining human settlements.

There is no direct relationship between Agents and sentinels except that they both work for the same entity against the humans.