Efficiency in processing algorithms of biological systems is actually one of the most relevant areas in computational biology. On the other hand, the technological advances in development of reconfigurable devices as FPGAs, offers today the possibility of designing really efficient implementations, which takes advantages of their particular characteristics as high speed, high integration density and rescheduling facility. It is well-known that a hardware implementation has better time efficiency than software development. This paper presents the FPGA implementation of Sankoff and Kruskal Algorithm that solves the “RNA problem”, which consists in searching the secondary ideal structure of RNA's chain.