The road bike I'm planning on buying is only available in 49cm and 50cm. Will that be okay given that my height is 5'8/9?
Very unlikely a 50cm (small?) bike will fit you. I'm about the same height and fit a 54/medium in most road bike models.
Some people about the same height with short legs fit a 52cm frame with a long stem fitted.
The manufacturer of the bike you are looking at should have a sizing guide that takes height and inseam measurements into account.
Don't compromise on bike size, get the bike you want that fits you. A frame that is much too small will be a pain to ride.
While it's likely that a 50 cm frame is smaller than you'd like (as others have said), there is one situation in which it would be what you want, and that is if you want a really aggressive aerodynamic position.
If you watch competitive cyclists, you will see that they generally position their handlebars quite a bit below the saddle height, especially for events where aerodynamics are very important such as time trials and draft-illegal du/triathlons.
If you are interested in having a very aerodynamic position with a large saddle to bar drop, you will need a bike with a short "stack", and a 50 cm might be about right for you. It depends somewhat on how long your legs are for your height.
That said, even pros often find aggressive aero positions uncomfortable to ride for long periods of time, and just getting into such a position requires that you be pretty flexible, so I wouldn't recommend it if you are just getting into road biking for the first time.
For reference, I'm a short-legged 5'6" and have regularly ridden frames as small as 47 cm, but for a comfortable touring bike (almost zero saddle to bar drop) I ride a 53-54 cm.