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There are inter-island flights by Lion Air, Merpati and Transnusa between Labuan Bajo, Maumere and Ende, with schedules – as well as airline - changes.
The so-called Transflores highway passes through the district capitals and major connection hubs, starting from Labuan Bajo up to Larantuka. Within the district capitals and larger towns, it is quite easy and cheap to handle short distances by hopping on and off the bemo (minibus). The ojek, a motorbike taxi often offered by young men who want to make extra income, is another option for shorter distances. As it is quite popular to be an ojek driver, you will also find these young chauffeurs in more remote places. The price is negotiable.
Travelling in Flores requires time and patience. Whatever transportation you may choose, you will meet relatively poor road conditions, even on many sections of the Transflores highway. The roads are often steep and curvy, which makes speed beyond 30 km/hr an exception.