Food safety in aquaculture is a crucial public health concern worldwide. Although Taiwan is a small island, the superior aquaculture techniques it employs allow Taiwan to maintain competitiveness in the Asian region. To achieve greater productivity, Taiwan’s aquacultures prefer intensive large-scale breeding operations, which can increase susceptibility to numerous pathogens. The use of several chemical substances with antimicrobial activity may be necessary to prevent and treat microbial and parasitic diseases. Because of this, residues of banned veterinary drugs namely chloramphenicol, malachite green and leucomalachite green and nitro furan metabolites may be present in shellfish available for consumption. Their toxicity for consumers, as well as their potential impact on the environment, could raise barriers to commercialization within Taiwan and for export. The objective of this review was to provide context and evidence for the use of banned agents in cultured shellfish, such as hard clams, freshwater clams, abalones and sea ears. Culturing of these shellfish emerged in Taiwan in the 1990s. Special attention was devoted to detecting the residual levels and violated ratios of illegally used animal drugs in shellfish products between 2010 and 2015. The results of these surveys indicated that the Taiwanese population is exposed to low (ng/g) concentrations of some banned veterinary drug residues, such as chloramphenicol, AOZ and SEM, through their consumption of shellfish. Among these samples, the highest ratio of positive identification of banned veterinary drugs was 12.8% of 39 samples in 2011, however, the residues were in trace amounts, with no immediate risk to consumer health. Therefore, continual monitoring of aquatic products is necessary to ensure food safety. Furthermore, these findings act as a reference for the health and agriculture authorities for improving administration and regulation.