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Southeastern has come out bottom in a national Which? survey of UK train firms.
In the first poll of its kind, the Kent-based rail operator scored just 40% for customer satisfaction.
That compares with Virgin Trains, which came out top with a customer score of 64%.
Among commuters, just 35% of Southeastern's users were happy with the service - that was also the lowest in the country.
Overcrowding and high fares were cited as key issues nationally, along with delays and cuts to services.
But, despite being unhappy, just 8% of users complained.
When they did, exactly half were unhappy with the way the complaint was handled.
Which? executive director, Richard Lloyd said: ""We don't have a choice of train company for most services, so it is infuriating when they let us down.
"With many of the rail contracts coming up for renewal over the coming year, the government and train companies must commit to improving passenger services across the board.
"While we found some encouraging examples of train operators getting it right, many have to work harder to ensure people get a good service and value for money."
A Southeastern spokesman said: “While we always take all customer feedback onboard, we are obviously disappointed with the survey results, as we’ve been working hard to make improvements for passengers over the past few years.
“Southeastern carries around 570,000 passengers every week day and more than 80 percent are commuters. This survey is based on 299 passenger responses - 87 of which are commuters.
“In the most recent National Passenger Survey, conducted by the independent watch-dog Passenger Focus and covering a much larger sample-size of, 83 percent of passengers said they were satisfied with Southeastern’s train services.
“At a time when we are running more train services than ever before and carrying more passengers, our punctuality figures are at an all time high (over 90%) and we are achieving the best results on this part of the network since punctuality records began.
“We know we have more work to do, but these results show that we are heading in the right direction and we trust our efforts will be reflected in future passenger surveys.”