Performance difference between Innodb and Myisam in Mysql?

That's a surprisingly large performance difference, but I can think of a few things that may be contributing.

My first suspicion would be that the original MyISAM table and/or indexes became fragmented over time resulting in the performance slowly degrading. The InnoDB table would not have the same problem since you created it with all the data already in it (so it would all be stored sequentially on disk).

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