The vector mosquitoes, Aedes aegypti and Aedes albopictus of dengue and Chikungunya fever are closely associated with human habitations and adapted to feed on human blood. They undergo larval and pupal development in natural and artificial freshwater collections in the urban and peri-urban environment. Although reports are available about the feeding behaviour of the thriving mosquito larvae, much information is still required to understand the successful survival of Aedes mosquitoes in small and temporary water collections. This study was undertaken to determine the co-existence and prevalence of Philodina roseola and other Bdelloid rotifers in the container habitats of Ae. aegypti mosquitoes. The investigation was conducted in 43 villages which belong to four districts in South India, affected by the epidemic of either dengue or Chikungunya fever. A total of 2093 houses and 12980 containers were examined for Aedes breeding and those containers with Aedes larvae were chosen for further investigation. The investigation showed that, the P. roseola was found associated in 502 (98.2%) containers, P. roseola along with other Philodina sp. in 126 containers (25%) and P. roseola along with other Philodina sp. and other Bdelloid rotifers found in 93 containers (19%). Since the members of the genus Philodina can survive desiccation, reproduce by parthenogenesis, can be transported by wind easily and more importantly, it can incorporate the genome of other organisms including viruses, understanding the co-existence and relationship of Philodina sp. with Aedes larvae would be helpful in the control of Aedes breeding and the control measures can be designed keeping the association of Bdelloids with Aedes in mind.