Our understanding of the role of nucleic acids in regulating the process of life is growing rapidly. As researchers delve deeper into the cellular activity of molecules such as microRNA, small interfering RNA, and long non-coding RNA, the oligonucleotide chemist is confronted with the challenge of synthesizing the tools needed to continue this work. Furthermore, new applications are being developed that require increasingly complicated oligonucleotide constructs. In this review, we explore the current challenges confronting oligonucleotide synthesis, describe the chemistry and the enzymology being developed in response to those challenges, and discuss future challenges as-yet unmet.