1646 Westminster Confession on Marriage

You can trace it back to Calvin's Marriage Ordinance of 1546 in Geneva. As others have noted, it follows the Levitical law, particularly Leviticus 18.

John Witte Jr. treats the subject in an article for the Calvin Theological Journal:

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwiUw-_9-fnVAhVLxlQKHRFhCGIQFggoMAA&url=http://www.johnwittejr.com/uploads/5/4/6/6/54662393/a140.pdf&usg=AFQjCNE_aY6i8w145rNUkYx0Fx_vooMh4g

 

I wouldn't say that it was original with Calvin because it reflects the Levitical code, and Luther had adopted a similar line, although it wasn't codified. However, Geneva's is the earliest ordinance I have found so far that codifies the Levitical rules.

Zwingli's Zurich adopted a code in 1525 that reformed marriage arrangements, but it did not specify the degrees of consanguinity or affinity that were allowed. Perhaps the degrees were understood and did not need explanation, although that ordinance deals at length with other requirements.

 

Exercising my rights to extend and revise my remarks:

In 1533 Parliament passed legislation that essentially followed the Reformation strictures on consanguinity and affinity. Those strictures, conveniently, recognized that a man could not marry his brother's widow, a most convenient finding for a king who had cast aside his first wife and married another woman.

Those regulations (which I assume were in line with the beliefs of the Reformation-leaning Thomas Cromwell) were confirmed in 1540 and reconfirmed in 1558 (after Mary's reign had re-established canon law).

But even among Protestants it was not settled exactly which relationships made an invalid marriage. Calvin, for example, considered that the Levitical list was an example and that similar degrees of relationship were also forbidden even though not mentioned by name.

The Anglican church sought to remedy the confusion by publishing a table in the Book of Common Prayer, one that was much more extensive that you might think would be warranted by the Levitical code.

So, based upon that, I would suggest that there was a common understanding — though not in the details — among the Reformers that the canon law prohibitions went far beyond scripture; that the Puritans who inserted the marriage language in the Westminster Confession were aware both of the the former (and perhaps from Calvin's influence, which was stronger than any of the other Reformers) and the importance of denying the legitimacy of Mary, in order to maintain the Protestant Ascendancy; and that confession article was a way to poke a thumb in the eye of the Book of Common Prayer without being caught out in the process.