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Abstract In contrast to sequence‐specific techniques such as polymerase chain reaction, DNA sequencing does not require prior knowledge of the sample for surveying DNA. However, current sequencing technologies demand high inputs for a suitable library preparation, which typically necessitates DNA amplification, even for single‐molecule sequencing methods. Here, electro‐optical zero‐mode waveguides (eZMWs) are presented, which can load DNA into the confinement of zero‐mode waveguides with high efficiency and negligible DNA fragment length bias. Using eZMWs, highly efficient voltage‐induced loading of DNA fragments of various sizes from ultralow inputs (nanogram‐to‐picogram levels) is observed. Rapid DNA fragment identification is demonstrated by burst sequencing of short and long DNA molecules (260 and 20 000 bp) loaded from an equimolar picomolar‐level concentration mixture in just a few minutes. The device allows further studies in which low‐input DNA capture is essential, for example, in epigenetics, where native DNA is required for obtaining modified base information.