Gastrotricha is a group of microscopic animals that are often overlooked in ecological surveys, despite their worldwide distribution across all oceans on Earth. The apparent incongruence between widespread distribution of microscopic animals and their life history is known as the ‘‘meiofauna paradox’’. This concept has been investigated in many meiofaunal groups and recent studies provide new insights revealing that the restricted distribution of these organisms is more common than was previously thought based on molecular diversity and muscular organization. The use of integrative morphological methods has been used in the past decades to increase the accuracy of species delimitation. In the present study we discovered a new species of the genus Kryptodasys (Macrodasyida: Macrodasyidae) from Capron Shoal, Florida, USA. For species delimitation, we used traditional light microscopy and Confocal Laser Scanning Microscopy (CLSM). The specimens of the new species show a unique reproductive apparatus and for the first time in the group, a muscular complex dedicated to the seminal vesicle is described. Also, a complex caudal organ composed of two compartments were observed. The complete muscular analysis added important novelties to the knowledge of muscular architecture of Macrodasyida group and to the phylum.