Fish embryonic stem (ES) cells derived from of blastulae (64 cell stage embryo) of Labeo rohita were propagated in culture and retained their ES cell-like properties after cryogenic storage (-196 °C, i.e., liquid nitrogen). Toxic effect of DMSO (dimethyl sulphoxide) on stem cells during preservation process has been reported to restrict therapeutic applications. In this study we reduced the concentration of DMSO and added the non-toxic cryoprotective agent (CPA) trehalose. Cryopreservation of ES cell colonies was done at 5, 25 and 52 passages with 0.2 M trehalose and 0.8 M (DMSO). A combination of both the cryoprotective agents (non-toxic and toxic) demonstrated better survival and recovery of ES cells than the DMSO used alone. Use of this CPA combination in the freezing media gave an optimum viability of more than 83 % in a slow freezing protocol. Trehalose showed a definite advantage over DMSO in terms of viability and intactness of ES cell colonies with evenly distributed morphology. There was no significant difference observed in the expression levels of cell surface markers like stage specific embryonic antigen-1 (SSEA-1) and alkaline phosphatase (ALP) between early and late passages after 60 days of post-thawing. More than 90 % of the ES cell colonies showed extensive expression of ALP and positive expression of SSEA-1 from an early stage of ES cells culture up to passage 52 (in our study) in the presence of leukemia inhibitory factor (LIF) and without feeder cells. Further, thawed ES cells showed a normal karyotype and maintained an undifferentiated state through out the study. This study on ES cell cryopreservation and subsequent retention of stem cell properties without feeder cells using a non-toxic cryoprotectant trehalose would be highly useful for future in vitro differentiation, manipulation of fish ES cells and as a model for mammalian ES cell culture.