This paper reports polymer-based apparatus with embedded flexible thin-film electrodes to monitor electrocardiogram (ECG) of zebrafish under mild or zero anesthesia. The apparatus were made of polydimethylsiloxane (PDMS) using the molding technique with molds formed by 3D printing. The system is capable of acquiring intrinsic ECG from multiple fish simultaneously, thus introducing a novel method to phenotypically assess the hearts' functionalities, supporting heart regeneration studies, drug screening and other related bioinvestigations using the zebrafish model. Smart algorithms were developed to facilitate data processing and analyses. The recorded ECG was compared with that of the same fish under full sedation and a proof-of-concept 4-chamber system was demonstrated. The process does not require a cleanroom, therefore being cost effective and holding promise to accelerate numerous studies in various disciplines using the zebrafish model.