locid country city
39409 US Aaronsburg
128426 US Aaronsburg
340356 US Aaronsburg
429373 US Aaronsburg
422717 US Abbeville
431344 US Abbeville
433062
Create a new table with new auto_increment field and just select them with GROUP BY into the new table
Not tested but should look like this:
INSERT INTO new_table(country, city)
SELECT country, city FROM old_table
GROUP BY country,city
EDIT: You could drop the old_table and rename the new_table afterwards.