Mary Mary quite contrary,
How does your garden grow?
With silver bells and cockle shells
And pretty maids all in a row.

The origins are steeped in history…

The Mary alluded to in this traditional English nursery rhyme is Mary Tudor, or Bloody Mary, who was the daughter of King Henry VIII. Queen Mary was a staunch Catholic and the garden referred to is an allusion to graveyards which were increasing in size with those who dared to continue to adhere to the Protestant faith. The silver bells and cockle shells were colloquialisms for instruments of torture. The ‘maids’ were a device to behead people similar to the guillotine. —Mary, Mary, Quite Contrary: Origin (Rhymes)

I found this on Circant, where I left the following comment:

The Mary Tudor suggestion sounds like it affirms the adage that history is written by the winners. The history of Protestantism in England wasn’t very long during the reign of Henry VIII’s daughter, and thus the phrasing “dared to continue to adhere to the Protestant faith” sounds very biased. Henry VIII burned plenty of Lutherans in his day; Microsoft’s Encarta characterizes Henry VIII’s reforms as chiefly political rather than theological.

http://encarta.msn.com/encyclopedia_761562628_2/Reformation.html.

Here’s a website with several additional interpretations of the rhyme.

http://www.rooneydesign.com/MaryMary.html