Exhibit 23.1
Consent of Independent Registered Public Accounting Firm
Bionano Genomics, Inc.
San Diego, California
We hereby consent to the incorporation by reference in this Registration Statement on Form S-8 of our report dated March 31, 2025, relating to the consolidated financial
statements of Bionano Genomics, Inc. (the “Company”) appearing in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024. Our report contains an explanatory paragraph regarding the Company’s ability to continue as a going
concern.
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/s/ BDO USA, P.C.
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San Diego, CA
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March 31, 2025
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