In A Moderate Answer to Dr. Bastwick’s Book, called Independence is not God’s Ordinance.1 Knollys, a congregationalist, writes:
Passing by many things less considerable, because I intend brevity, in the seventeenth page of the Doctor’s book, “There is a twofold question between them called Presbyterians and their brethren who are termed Independents; the first is, concerning the government of the church, that is to say, whether it be presbyterian dependent, or presbyterian independent? The second question is, concerning the gathering of churches.” 2
Setting up the discussion, you’ll notice Knollys quotes Bastwick as making a distinction between Presbyterians and Independents by referring to either, respectively, as presbyterian dependent or presbyterian independent. He goes on to write:
I intend not to strive with the Doctor about words, and therefore touching the two terms, to wit, dependent, and independent I shall only say this at present: that if by independent the doctor indeed means–as it does appear so to my understanding by many passages in his book he does intend–a presbyterian government, which has not dependence upon any in matters merely ecclesiastical but upon the Lord Jesus Christ, who is the head of the church, and if by dependent he also intends–as in many other passages in his book seemed to me to be his meaning–a presbyterian government, which has a dependence upon a supreme judicature of a common council of presbyters, and who must in matters ecclesiastical be subject unto the decrees, sentences, constitutions, and commandments of a common council, college or consistory of classical, provincial, or synodical presbyters, then I do conceive the Doctor has not proved, nor will he ever be able to prove, that the presbyterian government dependent is God’s ordinance.3
The key here is Knollys’ understanding of independency. An independent local church (congregational) is a body of believers with a presbytery (or elders), the congregation of which is not dependent on that elder body for ecclesiastical decision-making. Instead, it is an assembly that is wholly involved in ecclesiastical matters. Both congregation and eldership play a part in directing the affairs of the church.
Moreover, this elder body (or presbytery) does not preside over multiple churches as a “common council of presbyters,” but only have leadership jurisdiction within their own individual local churches to which they’ve been called.