On the standard version of my website I use the topmenu for main navigation. However, I cannot figure out how to change the mobileJoomla version to match (it seems to only have mainmenu with no option to change).

Is there any way to do this?

Thanks!

The menu shown by MobileJoomla is selected as a parameter of a module.
Although the modules are called Main Menu, the actual menu shown can be changed.
For example.
The home page shows two menus and the iphone shows one.
To get the other menu to show on the iphone you need to go to
extensions > Module manager >
and choose the Main Menu that has mod_mj_iphone_menu on the right hand side.
Click on it and on the screen you will see Parameters > Module Parameters > menu name.
This is a drop down menu, so select the name of the other menu and click save
You should then see the menu you want on the iphone.

Thanks after a long search you helped me to find the solution
I really appriciate

You are welcome. Thanks for posting.