Atapattu, who took over the one-day captaincy from Sanath Jayasuriya in early May, has kept the job despite Sri Lanka's failure this month to qualify for a home tri-series final for the first time.
"You can't judge a man on one series alone," said Lalith Kaluperuma, the chairman of selectors, when the 15-man squad was named on Tuesday.
"It was the batting that lost us the trophy. The top order just needs to regain its form."
The selectors made two changes, axing middle-order batsman Russel Arnold and all-rounder Kaushalya Weereratne.
Naveed Nawaz, a 29-year-old left-hander, who played the last of his three one-day internationals against India at the Oval in 2002, takes Arnold's place.
"Russel has been struggling for his form and we decided it was best for him to regain it before returning to the national side," said Kaluperuma. "Naveed has been batting well."
Dinusha Fernando, a 23-year-old uncapped swing bowler, replaces Weeraratne, who played just one game in this month's tri-series.
Fast bowler Dilhara Fernando has failed to recover fully from a lower back injury and was not considered for selection.
"The physiotherapist said he was not 100 per cent but we hope he will recover in time for the Test series," said Kaluperuma.
Sri Lanka are due to play three one-day internationals in the West Indies, starting on June 7 at Barbados, followed by two Test matches.
The squad for the Test series will be announced at the end of next week after a three-day practice game.
The squad: Marvan Atapattu (captain), Sanath Jayasuriya, Kumar Sangakkara, Mahela Jayawardene (vice-captain), Romesh Kaluwitharana, Tillakaratne Dilshan, Naveed Nawaz, Upul Chandana, Chaminda Vaas, Dharshana Gamage, Prabath Nissanka, Kaushal Lokuarachchi, Kumar Dharmasena, Muttiah Muralitharan, Dinusha Fernando.
