Alcaraz has only just returned to the first team following a lengthy spell out with a groin injury and any more time on the sidelines will come as a huge blow to Latics.
The return of Alcaraz coincided with an upturn in results as Latics have won five out of the last nine games but there is still plenty of hard work to do if they are to beat the drop and they need the defender fit.
Roberto Martinez is now waiting to hear the full extent of the damage and will be hoping and praying that it is nothing serious, with just five games of the season remaining.
"The injury to Antolin made for a very difficult afternoon for us at West Ham," he told the Wigan Evening Post. "He's got a soft tissue injury to the back of his hamstring, and so we'll assess him this week before discovering exactly how long he'll be out for.
"It's obviously a real negative note, and had an effect on how we wanted to play."