Yes, MySQL can use multiple index for a single query. The optimizer will determine which indexes will benefit the query. You can use
EXPLAIN to obtain information about how MySQL executes a statement. You can add or ignore indexes using hints like so:
SELECT * FROM t1 USE INDEX (i1) IGNORE INDEX FOR ORDER BY (i2) ORDER BY a;
I would suggest reading up on how MySQL uses indexes.
Just a few excerpts:
If there is a choice between multiple indexes, MySQL normally uses the
index that finds the smallest number of rows.
If a multiple-column index exists on col1 and col2, the appropriate
rows can be fetched directly. If separate single-column indexes exist
on col1 and col2, the optimizer will attempt to use the Index Merge
optimization (see Section 22.214.171.124, “Index Merge Optimization”), or
attempt to find the most restrictive index by deciding which index
finds fewer rows and using that index to fetch the rows.