0 (yes, in Kyushu they count from zero, go figure) and you buy your tickets from the rather inquisitive drivers on the train. Two ferries depart towards Kumamoto from different ports along this line but the most convenient is likely the one from Shimabara Port itself direct to Kumamoto Port. Walking maps from the stations to the ports are scrawled at each train station. After a rather scenic 30-60 minute cruise, you'll have to connect to a bus to actually reach central Kumamoto city.
Thats 4 modes of transport total and the times don't always match up so allow perhaps 4 hours for the journey unless you carefully plan it out using one of the big transport books at JR Nagasaki's ticket counter. Its all in there somewhere, I promise. Expect the entire trip to only set you back roughly 2500 yen, most of which goes to the Shimabara train company despite being the shortest leg. English-language signage along this route is minimal. Incidently, the final Kumamoto-bound ferries depart at 8PM daily, and one daily train reaches Shimabara a few minutes after that so don't get caught out
