Origin

During the time of Zerubbabel and Ezra there was a clear call to separation from foreigners and anything unclean. Some verses that clearly indicate separation during this time period is:

Ezra 6:21 "Then the children of Israel who had returned from the captivity ate together with all who had separated themselves from the filth of the nations of the land in order to seek the LORD God of Israel."

Neh 9:2 "Then those of Israelite lineage separated themselves from all foreigners; and they stood and confessed their sins and the iniquities of their fathers."

Although it is not absolutely clear when the name of "Pharisees" had actually been given to a religious group within Judaism, it seems like during these early times there were those who had intended to preserve the Law by having a stricter view of uncleanness, not only from the uncleanness of the heathen but from that with which they believed had affected the great portion of Israel.

As the priests and scribes were attempting to determine the inner development of Judaism after the captivity they apparently became more and more separated from the ways of the foreigners as the Lord had prescribed.

Sometime during the Maccabean period, groups within Judaism had sharply contrasted with each other and two religious parties were developed from them. The Sadducean party came from the ranks of the priests, the party of the Pharisees from the scribes. The Pharisees were more concerned with legal issues and the Sadducees with their social position.

It appears that during the Greek period, the chief priests and rulers of the people began to neglect the law; the Pharisees united themselves and became an association that made a duty of the law's meticulous observance.
They appear in the time of John Hyrcanus (135-105 B.C.) under the name of "Pharisees," no longer on the side of the Maccabees but in hostile opposition to them, because the Maccabeans' chief concern was no longer the carrying out of the law but extending their own political power.

The Pharisees had won the favor of the nation, and even Queen Alexandra, recognizing religious authority and seeking her own peace for her people, abandoned the power to the Pharisees even though Alexander Jannaeus had tried to exterminate them with the sword. This was a major turning point which brought the whole conduct of internal affairs into their hands. All the decrees of the Pharisees put away by Hyrcanus were reintroduced, and they completely ruled the public life of the nation. This continued for generations to come.

Even with the changes of government under the Romans and Herodians the Pharisees maintained their spiritual authority. Although the Sadducean high priests were at the head of the Sanhedrin, the decisive influence upon public affairs was in the hands of the Pharisees.

This is an interesting quote from Emil Schurer:

"They had the bulk of the nation as their ally, and women especially were in their hands. They had the greatest influence upon the congregations, so that all acts of public worship, prayers, and sacrifices were performed according to their injunctions. Their sway over the masses was so absolute that they could obtain a hearing even when they said anything against the king or the high priest, consequently they were the most capable of counteracting the design of the kings. Hence, too, the Sadducees, in their official acts, adhered to the demands of the Pharisees, because otherwise the multitude would not have tolerated them"

-Schurer, History of the Jewish People in the Time of Christ, Part. 2, 2:28). Edinburgh: T. & T. Clark, July 1987.