The suspects, both aged 21, were arrested at 19.30 BST on Thursday at separate addresses in Southport.
Computer equipment was seized and electronic devices were forensically examined at the properties in Moreland Drive and Old Park Lane.
The men will be questioned at separate police stations on suspicion of committing cyber-crime offences.
The investigation was led by the North West regional organised crime unit Titan supported by the National Crime Agency (NCA), Europol and the Federal Bureau of Investigation (FBI).
The suspects were kept inside the properties while Titan officers examined various electronic devices using a mobile cyber forensic lab provided by Europol.
Two men have been arrested on suspicion of supplying software for use by computer hackers.