Can I charge a different markup to different customers for the same hotel or flight?

Yes, in most systems you can. Rather than one markup applied to everything, you keep a set of rules and the system decides which one applies at the moment the price is shown, based on who is looking at it. A walk in customer, a sub agent in your network and a corporate account can all see the same hotel at a different final price, without you touching the booking by hand.

Markups are usually set as either a percentage or a flat amount, and you can normally narrow them down further, by supplier, by product type such as flights or hotels, by country or by the group the customer belongs to. The part that trips people up is what happens when a customer matches two rules at once, for example a corporate client who is also in a promotional group. Decide the order of priority when you set the rules up, because the system will follow whatever order it is given rather than what you meant.

There are limits and they usually come from the supplier rather than from the software. Some fares and rates reach you as net rates, which you are free to mark up as you like. Others arrive as published or agreed prices where your contract does not allow you to change what the customer sees, and in those cases your earning is the commission rather than a markup you set. It is also worth deciding early whether your markup is refunded when a customer cancels, because that affects both your refund wording and what you eventually settle with the supplier.

Before you go live, write down the customer groups you actually sell to, check your supplier agreements for which rates permit a markup, then run one test booking for each group all the way through to the invoice and a cancellation, so you can see the markup behaving the same way at every step.