Two clocks are asynchronous when it is impossible to determine their relative phase.
For example, two clocks generated by separate oscillators on the board and entering the FPGA by means of different input ports have no known phase relationship. They must therefore be treated as asynchronous. If they were generated by the same oscillator on the board, this would not be true.
In most cases, primary clocks can be treated as asynchronous. When associated with their respective generated clocks, they form asynchronous clock groups.