Here are a couple of paragraphs from this website that may help:
It is difficult to trace Baptist churches down through history. Some Baptist historians, have made attempts at doing this, but in many cases those they refer to groups as early Baptists who did not in fact hold to pure Baptist beliefs as held today. They try to establish that "according to history, Baptist have an unbroken line of churches since Christ". (Quote from Dr. J.M. Carroll's booklet "The Trail of Blood") These historians, in an attempt to show an unbroken line of Baptists in history, have embraced groups which were clearly not doctrinal sound. In the simplest of terms a true Baptist assembly is one which follows the New Testament as his sole authority for his faith and practice. Whether these groups of believers called themselves Baptists or not, if they were doctrinally pure following the New Testament for their faith and practice they were New Testament churches and thus they can be called Baptistic. The point is there were true New Testament churches called by various names, before assemblies used the name Baptist. Some Baptists such as the the Landmark Baptist conclude they trace their history back to John the Baptist who was the first Baptist. However, John the Baptist was an Old Testament saint and the last Old Testament prophet (Matt. 3:3). He did not belong to, nor was part of the any "ekklesia." Yes he baptized, but His baptism was the baptism of repentance (Matt. 3:2) for Jews who were preparing for coming Messiah and Kingdom God had promised them. John was beheaded by Herod (Matt. 14) before the Lord Jesus announced the coming establishment of the "ekklesia." (Matt 16:18). John was God's true prophet and the forrunner of the Messiah Jesus Christ, but he was not a part of the dispensation of the institution of the local church.In examining many so-called early "Baptist" churches you find many doctrinal errors and false teaching. Surely, no church that practiced false doctrine as many of these groups did can in truth be called a Baptist church. It is my conviction that it is not possible to "trace" an unbroken line of Baptist churches from Christ until today. However, let me strongly say there has always existed an unbroken line of churches who have not erred from the faith, and been true to the Bible, God's Word. In fact Jesus emphatically stated in Matt. 16:18, concerning the church, that even "the gates of hell shall not prevail against it." These churches have always existed from the time of Christ and the Apostles until today. To call these people Baptists or Baptistic, in the sense that the believed the Bible and followed it as their sole authority for faith and practice, in the way same true Baptist churches do today, is acceptable, although it serves no purpose. To go so far as to say there is a unbroken line or succession of Baptist churches from the time of Christ until today cannot be shown from history.
This is pretty much my view of things.
The linkage would be theological rather then organizational.