Cardinality as returned by SHOW INDEX
is an estimate, mostly used by the optimizer to build the query execution plan:
http://dev.mysql.com/doc/refman/5.0/en/show-index.html
Cardinality
An estimate of the number of unique values in the index. This is updated by running ANALYZE TABLE or myisamchk -a. Cardinality is counted based on statistics stored as integers, so the value is not necessarily exact even for small tables. The higher the cardinality, the greater the chance that MySQL uses the index when doing joins.
Depending the way you populated your table, those values might be outdated. And, to paraphrase the doc, in that case you should use ANALYZE TABLE
to update those statistics.