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The buses are awesome. They come every 6-10 minutes or so depending on the route and the lines (28) criss-cross all over the city so it is possible to get wherever you are going on just 1 or 2 buses. There are no transfers but then a single ride is $0.25 so they aren't really needed. The buses are as modern and clean as any I have seen anywhere else in the world including Canada or the States (just the usual graffiti). And have not been on a single broken down bus yet! The city is in the process of adding new more environmentally friendly buses. I have not yet seen any animals on the local buses (other than the small dogs in bags). Don't know too much about the inter-city buses but they all look comfortable and I believe they only cost about $1 per hour of travel.

The bus system in Cuenca is great.  No livestock etc. It is reliable and frequent except for on Sundays (which has a different schedule).  It can get crowded at certain times but its never that bad and the buses are frequent enough (and multiple lines)that you could wait for the next if you wanted. There are a number of bus lines that will take you all over the city.  You can get a good bus map at ITUR which is in Parque Calderon in Cuenca.  To go outside of Cuenca there are an array of busses you can take.  For the most part they are not extreme.  And if you want to take a costal trip then I recommend the LIBERTAD PENINSULAR C.L.P. buses which are pretty nice with A/C and a movie if you get a direct bus (but you can't take this from Cuenca, go to Guayaquil).  And the Manglaralto Bus is not that bad either but its more of an open windows, random venders on and off again, roller-coaster, watch you stuff kind of ride. Not bad tho.