The pair, aged 21 and 25, were arrested on Saturday evening. Both have been charged with eight counts of criminal damage and with possessing an article with intent to damage property.
They are due to appear at Coleraine Magistrates' Court on Monday.
A series of slogans were discovered in streets around Larne, which is located about 22 miles north of Belfast, on Saturday.
"Larne says no to Irish Sea Border", one piece of graffiti read. At around 9.40pm that evening police received reports that two men had been spray painting graffiti on a property in Main Street.
Officers responded to the report and located two males in the Main Street area of Larne. They then searched a vehicle in the area and a number of items were seized and taken away for examination.
Officers subsequently arrested two men in the Church Road area of Larne on suspicion of offences, including criminal damage and possessing of an article with intent to damage property.
Police are also investigating further reports of graffiti in the town on Point Street, Bank Road and Redlands Road.
It came just six days after staff at Belfast and Larne ports were removed over threats to their safety.
Inspections at both ports were suspended amid an “upsurge in sinister and menacing behaviour in recent weeks”.
A separate piece of graffiti had appeared in Larne describing customs officials there as "targets".
Officials from Mid and East Antrim Council, Stormont's Department of Agriculture and the EU Commission all stopped working at the facilities, which conduct checks required as part of Brexit's controversial Northern Ireland Protocol.
Environmental health staff from Mid and East Antrim Council returned to their duties at Larne Port on Friday.
It has not been confirmed when the other officials, who work at both Larne and Belfast, might return to work.