The two airlines' combined network is expected to cover 240 destinations by 2020, served by a combined fleet of 380 aircraft, the statement added.
Work on combining a number of areas such as network planning and frequent-flyer programmes is already underway and the group said it expects the first new code sharing agreements to be in place in the final quarter of this year.
Sheikh Ahmed Bin Saeed Al-Maktoum, Chairman and Chief Executive of Emirates Group and Chairman of flydubai, said "Both airlines have grown independently and successfully over the years, and this new partnership will unlock the huge value that the complementary models of both companies can bring to consumers, each airline, and to Dubai".
The new agreement comes as Emirates' profits fell by more than 80 percent to $340 million in the last fiscal year due in part to a slump in demand and U.S.travel restrictions.
"The new model will give flydubai customers seamless connectivity to Emirates' worldwide destinations spanning six continents".
"Both airlines have grown independently and successfully over the years and this new partnership will unlock the enormous value that the complementary models of both companies can bring to consumers, each airline and to Dubai". "For Emirates' customers, it opens up flydubai's robust regional network".
The current joint fleet size is 317 with a combined network of 216 unique destinations. Emirates, the largest airline in the Middle East, flies to 157 destinations with 259 planes, while low-priced airline Flydubai reaches 95 destinations with 58 planes.
Dubai has been looking at placing the two government-owned carriers under a single structure for several months.
Teams from Emirates and flydubai are now working on several initiatives spanning commercial, network planning, airport operations, customer journey, and frequent flyer programmes alignment.