Malachite green (MG), one of the toxic triphenylmethane chemicals, has been used worldwide in aquaculture because of its low cost and high efficacy in bacteriostasis. However, the residue of MG may cause carcinogenic, teratogenic and mutagenic effects. Traditional methods for MG detection are relatively complex, which require complicated operations of pretreatment, take a lot of time -, and need expensive instruments. Thus a rapid and simple detection method needs to be developed. Aptamers are the functional single stranded DNA or RNA molecules which have high-affinity and specificity in binding capabilities towards a vast range of targets. Therefore, aptamers have been widely applied as recognition elements for biosensor in recent years. Gold nanoparticles (AuNPs) with high extinction coefficient and surface plasmon resonance have been used in colorimetric detection systems. In this work, a facile colorimetric aptasensor for highly sensitive detection of MG based on aptamer and AuNPs was developed. In the absence of salt, AuNPs agglomerated in salt with the absorption peak of UV-vis spectrum shifted from 520 nm to 690 nm, and the solution color changed from red to blue. However, the complexation of RNA aptamer with AuNPs prevented the nanoparticles from aggregation in a high-salt solution because of the electrostatic interaction between RNA aptamer and AuNPs. In the presence of MG, RNA aptamer could specifically bind with MG, causing AuNPs aggregation with blue in color in salt. With the increases of MG concentrations, the values of A520 decreased and the values of A690 increased, and the color of the solution gradually changed from red to blue. Taking advantage of this sensing technique, MG could be detected by naked eyes or UV-Vis spectroscopy within one hour. The differences of A690/A520 with and without MG in the detection systems were used as the detection signals. The results showed that the linear range of MG was 0.6 to 12.5 μmol·L-1 at the optimum conditions of 0.2 mol·L-1 NaCl, 10 μmol·L-1 RNA and 7 nmol·L-1 AuNPs. A linear equation of Δ(A690/A520)=0.06C-0.01 was obtained with a correlation coefficient (R2) of 0.993. The detection limit was 0.04 μmol·L-1 (3α/κ, n=9). The method had good selectivity for MG detection. Furthermore, the developed method was successfully applied to the detection of MG in aquaculture water with excellent accuracies. The results indicated that the developed method has significant potentials for trace MG detection in real samples.