One of the best 'regional history' museums we've been in, in South and Central America.
$57 peso entrance per person. You can also get an audio guide for $50 pesos in English or $40 pesos in Spanish. If you can read Spanish there is an unbelievable amount of information on signs and boards in the museum and cards in the doorway with even more information. There isn't much information in English though so may be worth paying for the audio guide as there are so many interesting back stories and insights into Oaxaca region's past.
There was an interesting modern art exhibition by two Brazilians downstairs, which captivated our attention for longer than most modern art does... then there were dozens of exhibitions on the region's history upstairs, which were well organised and well signed.
It's free to take in a camera (no flash) but there is a fee for video cameras ($$45 pesos I think).
The botanical gardens tour is no longer free and now has a separate office around the corner from the museum (walk round the building past the museum and away from the church). It is 100 pesos for a tour in English or 50 pesos for a tour in Spanish (it is by guided tour only). There are set times - the Spanish tours are almost every hour and the English tours are every other day (I think Tuesday, Thursday and Saturday) at set times (possibly 11am and 1pm, from memory). We didn't do the botanical garden tour, but you do get a good view of the cactus beds from the museum.
We spent 2 hours in the museum and rushed round a bit. You can't bring food or drink in, so worth going just after breakfast or just after lunch so you can keep going as long as possible :-) We could definitely spend another afternoon there as there is so much to learn.
What topped off the experience is that it is in the former monastery, so the building is stunning. And there are also great views over the plaza.
This review is the subjective opinion of a TripAdvisor member and not of TripAdvisor LLC.