Auckland Transport said the new system, dubbed "simpler fares", would help make it easier for people using multiple forms of transport to get around.
Group manager of the agency's Metro brand development, Colin Homan, said the colour-coded zones along with a new fare table would help people better calculate the cost of their fares before they travel.
The 13 fare zones are Hibiscus Coast, Upper North Shore and Lower North Shore in North Auckland and Helensville, Huapai and Waitakere in West Auckland. In Central Auckland there is the City, Isthmus and Waiheke and in East Auckland, there is the Beachlands zone. In South Auckland there are Manukau North, Manukau South and Franklin.
"Simply add up the number of zones you are travelling through and use the fare table to work out your fare."
During a journey people can use up to five buses or trains within four hours, with up to 30 minutes transfer time between each trip.
Homan said the simpler fares would become increasingly important as Auckland Transport rolls out new public transport over the next two years, beginning with South Auckland later this year.
The fare system has been rolled out the same time as an update to Auckland Transport's app which the agency said was more user-friendly.
SkyBus services are excluded from the new system.