A clock signal generation and distribution system for a prototyping apparatus of an electronic system comprises at least one clock signal generation and distribution subsystem for distributing at least one clock signal to the prototyped electronic system implemented by the prototyping apparatus through a clock signal distribution network of the prototyping apparatus. The at least one clock signal generation and distribution subsystem comprises a clock source selector for selecting the at least one clock signal to be distributed to the prototyped electronic system among a group of source clock signals, the group including at least one first source clock signal derived from the prototyped electronic system and at least one second source clock signal not derived from the prototyped electronic system.