The development efforts aimed at fishers and fish farmers in the developing world focused on helping them to build their capacity to adapt to climate change. Small indigenous fishes (SIFs) have high consumer preference, and hence they demand high price in Northeastern region of India. An experiment was conducted to assess feasibility of culturing high value SIFs (Amblypharyngodon mola, Gudusia chapra and Puntius spp.) along with Indian major carps (IMC) in pens installed in a floodplain wetland (beel) of Assam. Five pens of 10 m x 10 m (100 m2area) were constructed in 47-Morakolong beel (seasonally open wetland), Morigaon district, Assamwith low-cost and locally available materials. The IMC (Catla catla, Labeo rohita and Cirrhinus mrigala) were stocked at 2:1:1 ratio @ 3 no./ m2 in all the pens. Five different species combinations (treatments) were tested i.e., P1 (IMC only), P2 (IMC +A. mola @ 30 no./ m2), P3 (IMC + G. chapra @ 20 no./ m2), P4 (IMC + Puntius spp. @ 20 no./ m2) and P5 (IMC + all three SIFs @ 1/3rd of the original stocking density of each species). The stocked fishes were fed with formulated pelleted feed containing 30% CP @ 3-4% body weight of IMC twice daily and cultured for five months. The highest fish production was obtained from P3 (1.48 kg/ m2) followed by P2 (1.46 kg/ m2), P5 (1.3 kg/ m2), P4 (1.08 kg/ m2) and P1 (1.05 kg/ m2). Economic analysis of the pen culture operation indicated that culturing IMC with G. chapra or A. mola was the most profitable one with B:C ratio of 1.54 and 1.51, respectively. Rearing of IMC with all the three SIFs was observed to be more economical (B: C ratio of 1.35) than culturing IMC alone. However, culturing IMC alone or with Puntius spp. recorded similar returns. All the three SIFs bred naturally in the pens as indicated by the presence of various size range of the fish. Our result indicated that culturing of locally preferred high value G. chapra and A. mola along with IMC in pens was economically profitable yielding higher returns than culturing IMC alone. In conclusion, pen aquaculture practice in floodplain wetlands of Assam can be adopted as polyculture of SIFs with major carps instead of culturing only major carps for additional income of the wetland fishers and conservation of SIF in the changing climatic scenario.