In Challenge mode, the player starts a zoo from scratch and will be given random challenges which can be accepted or rejected.

In Campaign mode, the player plays through a scenario in an existing zoo and is assigned different goals to complete, such as achieving a certain fame level, caring for rescued animals, or breeding endangered species. Zoo Tycoon 2 features three gameplay modes: Campaign, Challenge and Freeform.

Guests will visit the zoo to see the animals, and they also have needs that need to be fulfilled through scenery and buildings (hunger, thirst, bathroom, seating, entertainment). The Zoo Tycoon 2 gameplay revolves around creating suitable exhibits for animals through habitat modifications (ground cover, water, elevation, foliage and rocks and a variety of items including food, enrichment and shelter) which fulfill the animal's needs (habitat, hunger, thirst, stimulation, privacy, sleep, social, exercise). See List of animals in Zoo Tycoon 2 for a full list of animals in the Zoo Tycoon 2 games.

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