KEYWORDSMicro uidic biochip; Physical design; Architecture.Abstract. Micro/nano uidic biochips are used to automate the clinical diagnosis, DNA sequencing, drug discovery, and real-time bio-molecular recognition. One of the attractive usages of biochips is Lab-On-Chip (LOC). Lab-on-Chip technology is a promising replacement for biomedical and chemical apparatus. Two main types of micro uidic-based biochips are used: continuous-ow-based and digital micro uidic biochips (DMFB). In DMFBs, liquids, in the form of droplets, are controlled independently and concurrently over a two-dimensional array of cells (or electrodes). Digital micro uidic biochips are of high ability to con gure and for fault tolerance. In this paper, a new architecture for DMFB with an aim of making a balance between the parameters of exibility, e ciency, cost, and completion time of biological experiments is presented. In the new architecture, a FPGA-based structure is used, which increases exibility and parallelizing assay operations. Experiments show that the execution times of scheduling, routing, and simulation have improved by about 2.54%, 18.76%, and 12.52%, respectively, with 21% overhead cost in the number of controlling pins.