The year-long service which officially launched last week will provide businesses in the South with a direct route into Bavaria’s capital city.
Munich is one of Europe’s leading cities when it comes to sport, culture and economics and many businesses in the South have business interests in and around the city.
It is also one of the words largest financial centres and famously the home of BMW, making it a key destination for businesses operating in the automotive sector.
Dave Lees, managing director at Southampton Airport, said: "Services into Germany are always in high demand so it is fantastic to be able to offer this route into Munich with Flybe.
"Many local businesses have strong connections in Munich and it is also a key tourist destination, especially for the upcoming Oktoberfest as well as the German Christmas markets as we move into winter."
Vincent Hodder, Flybe’s chief revenue officer, added: "Our new Munich service also gives our Southampton travellers the flexibility to conveniently link with and conduct important business with this key German centre of commerce and, for leisure customers, the opportunity to explore the many attractions the region has to offer.
"We are looking forward to welcoming all our new passengers on board."
According to the latest research by the Department for International Trade shows Germany is the UK’s largest export market in Europe and second largest globally after the US.
The UK’s market share of German imports is around 4.4%.