run mysqldump with "--skip-opt" to get the 2 dumps files i.e:
mysqldump --skip-opt -u $MY_USER -p$MY_PASS mydb1 > /tmp/dump1.sql
mysqldump --skip-opt -u $MY_USER -p$MY_PASS mydb2 > /tmp/dump2.sql
compare using these diff options:
diff -y --suppress-common-lines /tmp/dump1 /tmp/dump2