Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We consent to the incorporation by reference in this Amendment No. 1 to Registration Statement No. 333-239360 on Form S-3 of our report dated March 10, 2020 relating to the financial statements of Bionano Genomics, Inc., appearing in the Annual Report on Form 10-K of Bionano Genomics, Inc. for the year ended December 31, 2019. We also consent to the reference to us under the heading “Experts” in such Registration Statement.

/s/ Deloitte & Touche LLP

San Diego, California

July 1, 2020