Could be one or more of related bottlenecks:

Do you have optimized statistics for the table?

are you using transactions?do you exclusively lock the whole table or do do use page level locking?
If you lock the whole table exclusively for each transaction you do have a big issue.
There is also possibility that transactions within a session are getting hung and being zombied but not the session itself

ISAM tables are notorious for overflow pages,better try a btree structure

Are your queries using the indexes? are you using functions in the where clause?

what is the query execution plan's estimation on Disk I/O resources for the given queries?

In reply to Re^3: Sleeping mysql connections after finish and disconnect by nikosv
in thread Sleeping mysql connections after finish and disconnect by drusher

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