In general algae shows ability to survive in wide range of environmental conditions. Under natural condition, they usually grow in the mixed community. Many algae have a special adaptibility to form net in water bodies and on surfaces were water falls continuously. This communication deals with the dynamics of the net forming and non net forming algal species from different water bodies. Total 16 samples of algae collected from Varanasi and Chandauli district, and their species varification done, of them 14 species were declared, as two similar species were sampled. Out of them 6 were mat forming and 8 non mat forming species. Sampling done from two different types of water habitat i.e., stagnant and running. pH of the water bodies varied from 7 to10. ISSR marker based diversity studied for 11 algal species which include 6 mat forming and 5 non mat forming. Total 97 bands amplified from 12 ISSR primers of them 77 bands were polymorphic. Number of amplified band varies from 6 to 11 with an average 8.08 band from each primer. PIC ranged from 0.407 to 0.654 and there mean is 0.536. Jaccord’s similarity coefficient varied from 0.60 to 0.88 with mean value 0.74. Algal species grouped in two major groupes. This study provides information for future exploration and collection of different algal species in Uttar Pradesh, India, and needs more research to find out industrial application of mat forming algal species.