Fish can adapt to a wide range of temperature changes, however, the molecular mechanisms that underlie these adaptations are not fully understood. In this study, fluorescently labeled differential display (FDD) technique was used to detect mRNAs that are differentially expressed in hepatic tissues of Tilapia zillii fish subjected to a temperature reduction regime that combined both accelerated and stationary cold stresses. The two arbitrary primers (DD1 and DD2) with the Oligo d(T)23-C generated a total of 18 and 37 unknown messenger RNA (UMR) bands, respectively. Both DD1 & DD2 arbitrary primers with oligo d(T)23-C scored four stress-related unidentified fragments after refining. Using the two arbitrary primers with the Oligo d(T)23-G, a total of 371 and 372 UmRs were yielded, respectively. Both arbitrary primers scored nine stress-related unidentified fragments after refining. All UmR were tested for its correlation to time and temperature factors scaled for the current experiment, only four were found to be correlated for both factors. Thus, T. zillii responded to temperature reduction by adjusting the expression of a set number of genes that may be required for their adaptation and tolerance to low environmental temperature.