How did the Pueblo people trace their lineage, through the father or mother?

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It was always my understanding that native people always takes the blood of their mother.

Unless there is something I do not know about Pueblo people, or understand your question very well, everyone's heritage is traced through both parents. To only trace your lineage through one parent is only half of who you are. You are not 100% your father and 0% of your mother. You are 50-50.

While what 69Cherokee said is true, I think this question is more along the lines of how did the Pueblo people HISTORICALLY trace their lineage.

While I can't speak at all to this culture, this is an excellent question. If you get into hardcore genealogical work, especially more than a couple hundred years ago, it is very important that you DO understand the cultural/historical lineage tracing procedures of the culture, region and for that time!

Judiasm for example is matrilinear, that is lineage is traced through the maternal lines. In historical formal ancestry presentations, the maternal line is maintained, the paternal side isn't (except through the patronymic form of a name). One of the common cultural arguments for matrilineage is that "you know who the mother is".

Sometimes the tracing methods are very different even within a parentage. European nobility is a good example. It wasn't uncommon for a noble to have 20 or more children - with wives (a more recent "institution" than many realize), consorts, chambermaids, an available woman [I guess rank has it's priviledges].

However, only a few (who would be considered by the father to be "heirs") would be traced through the father. Often the mother may be mentioned in some historical document, maybe, but isn't maintained in lineage records. Unless of course she was from another noble family and there were political reasons to do so. But the other 17 of these children would likely be traced through the mother (and given her probably low societal standing, are not traced at all). Also, marriage as a "monagomous joining of two people in love" is a really recent institution. So understanding the tracibility conventions used at the time is important because you will often see a Noble and a wife and a whole bunch of children. This doesn't mean the wife was the mother. In many societies, children from different females often resided in the household of the "declared" father, even though the "wife" wasn't the mother. Other children were just left with the mother, given no association with the noble.

So this is a great question and one you have to keep in mind when doing hard core genealogical research on historical documents.