The automorphism group of an elliptic curve over an algebraically closed field is well known. However, for various applications in coding theory and cryptography, we usually need to apply automorphisms defined over a finite field. Although we believe that the automorphism group of an elliptic curve over a finite field is well known in the community, we could not find this in the literature. Nevertheless, in this paper we show the group structure of the automorphism group of an elliptic curve over a finite field. More importantly, we characterize subgroups and abelian subgroups of the automorphism group of an elliptic curve over a finite field. Despite of theoretical interest on this topic, our research is largely motivated by constructions of optimal locally repairable codes. The first research to make use of automorphism group of function fields to construct optimal locally repairable codes was given in a paper \cite{JMX20} where automorphism group of a projective line was employed. The idea was further generated to an elliptic curve in \cite{MX19} where only automorphisms fixing the point at infinity were used. Because there are at most $24$ automorphisms of an elliptic curve fixing the point at infinity, the locality of optimal locally repairable codes from this construction is upper bounded by $23$. One of the main motivation to study subgroups and abelian subgroups of the automorphism group of an elliptic curve over a finite field is to remove the constraints on locality.