Both phones will run iOS7, the new version of Apple's mobile operating system. The OS will also be available as an update to iPhone 4 and later phones from September 18 at no cost, and that led Cook to make a prediction.
"iOS7 will quickly become the world's most popular mobile operating system," he said.
The operating system features a visual refresh with new icons, access to search throughout the phone, a drop-down notification page and an improved camera application, said Craig Federighi, Apple's senior vice president of Software Engineering.
Both the iPhone 5C and iPhone 5S will be important to Apple as it tries to shore-up and increase its share of the fast-growing smartphone market.
While the iPhone is often ranked as the best-selling smartphone, the large number of phones put on sale by competitors like Samsung are together attracting more customers. That means Apple's market share is falling.
In the April to June quarter, 31.2 million iPhone units were sold, up from 26 million in the same period of 2012, but despite the healthy rise the company's share dropped to 13.6 percent of the global market, down from 16.6 percent, according to Strategy Analytics.
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