Experiments were conducted to find out the applicability of autotrophic biofloc system for the culture of rotifer (Brachionus plicatilis). Normal autotrophic microalgae (MA) based culture system was compared with normal heterotrophic biofloc system (BF) without microalgae input and autotrophic biofloc system (BA) where biofloc was supplemented with microalgae initially. All the three systems were inoculated with rotifer and were cultured without any inputs such as feed, water, etc. The daily survival in terms of rotifer numbers and egg bearer percentage were noted till the perishing of the cultured organism. Simultaneously, the survival and percentage egg bearer were plotted graphically to obtain a growth curve and recruitment curve of rotifer in different systems. Growth curve of rotifer in different treatments shows there was no significant increase in number of survivor ml-1 in the first two days which may be the lag phase. MA as well as BA showed rotifer survival up to 6 days whereas in the BF it was 4 days. The peak production was observed on the 4th day in MA (90.00±5.00 nos.), BA (33.67±0.88 nos.) and BF (29.00±2.31 nos.) followed by the peak in percentage egg carriers on the 3rd day. There was no significant difference in the protein content of the rotifers harvested from the treatments. However, slightly higher values were observed in the BA (26.27±1.70%) and BF (24.33±1.03%) compared to MA (23.33±0.45%). Similarly, carbohydrate content did not differ significantly but slight difference was observed, the lowest in MA (36.27±0.94%) compared to biofloc based treatment groups, i.e., BA (38.57±0.43%) and BF (39.70±0.44%). The study concludes that B. plicatilis can survive in biofloc based systems and autotrophic based biofloc system can be considered as an alternative system for rearing of rotifer.