Commuters from Brighton, Hove and Portslade were delayed for up to an hour on their way to work this morning after signal problems caused problems in the Haywards Heath area.
Some services were cancelled or disrupted – missing out stations – as rail staff worked to fix the problem.
Earlier a trespasser on the tracks was blamed for trains from the Portsmouth area to Hove being held up or skipping stations.
Southern said: “Owing to signalling problems at Haywards Heath, we are now able to run southbound from Three Bridges towards Haywards Heath.
“Services via Haywards Heath are subject to short notice alterations, cancellations and delays of up to 60 minutes.
“Tickets are being accepted on Southeastern services between Hastings and London and Southern and First Capital Connect services are passing each other’s tickets.”