21 October 2016 Last updated at 15:03 BST
In 2008, about 40 were recorded on the seahorse study site at South Beach in the bay, but none have been spotted there since 2013.
Miranda Krestovnikoff has been investigating for Inside Out and speaking to Neil Garrick-Maidment, from the Seahorse Trust, and the Royal Yachting Association's Emma Barton.
Spiny seahorses may soon be locally extinct at Studland Bay in Dorset, according to the Seahorse Trust.