Just before the first Jewish War with Rome (67-70 CE) that culminated in the loss of the Second Temple, Judaism had a rich diversity, as documented by the New Testament, the writings of Josephus, the writings of Philo, and the Dead Sea Scrolls. The New Testament, for example, refers to the Pharisees, the Sadducees, the scribes, and the lawyers. Quasi-political groups include the Herodians and the Zealots. Josephus adds the Essenes and the Therapeutae. In the book of Acts, we encounter the Hellenists and the Hebraists as well as the proselytes and the God-fearers.
Tragically, much of this diversity did not survive the war with Rome. The Sadducees, for example, were closely connected with the priesthood, and many priests committed suicide in the flames of the burning temple. The Romans hunted down and wiped out the Essenes as well as the zealots. The Herodians ceased to exist because the need to support the Herods as the legitimate ceased to exist.
Thanks to Jonathan ben Zakki, the Pharisees survived the war, and their doctrinal positions and approach to the Scriptures became the new Jewish orthodoxy. The rabbinic Judaism we read in the Mishnah is Pharisaic Judaism.