Biosynthetic bubbles produced by floating microorganisms, such as bacteria and algae, have recently attracted wide attention as novel ultrasound contrast agents owing to their significant potential in ultrasound imaging and acoustic reporter gene-based imaging. However, the acoustics properties of these bubbles are unclear. In this study, we developed a finite-element model to describe the oscillation of nonspherical biosynthetic bubbles composed of a gas core encapsulated in a protein shell. In this model, the elastic properties of the bubble shells were characterized in terms of the density, thickness, Young’s modulus, and Poisson’s ratio. Theoretical calculations were performed for a single bubble and an assembly of randomly oriented bubbles. Our results demonstrate that (1) there are many types of surface oscillation modes for nonspherical biosynthetic bubbles, and a systematic relationship exists between the surface modes and the resonance frequencies; (2) the bubble shell shape has a significant effect on the acoustic behavior; (3) the resonance frequency of an ellipsoidal bubble decreases with the decrease in its polar radius-to-equatorial axis ratio; and (4) the acoustic scattering of a randomly oriented suspension is isotropic at and below the first resonance frequency. Our findings provide physical insight into the biomedical applications of biosynthetic bubbles and can be used to optimize the acoustics properties of such bubbles.