In this study, we investigated the biological toxicities of two crystalline phases and differential sizes of $TiO_2$ nanoparticles (anatase; 7-8 nm, 12-14 nm, and 17-23 nm, rutile; 80-100 nm, 150-200 nm, and 500 nm) using the zebrafish in an aquatic ecosystem. The zebrafish morphants that survived exposure to the $TiO_2$ nanoparticles exhibited incomplete notochord formation, with epidermal malformations observed in the larvae exposed to the anatase crystal type of $TiO_2$ nanoparticle (12-14 nm). In particular, there was more apoptosis after exposure to specific particle sizes (12-14 nm) than there was with the larger particle size (17-23 nm) of the anatase crystal type of $TiO_2$ nanoparticles. In addition, the group exposed to the anatase crystal type $TiO_2$ nanoparticles (7-8 nm, 12-14 nm, and 17-23 nm) showed more accumulation in the M1 phase of the cell cycle than did the control group. We observed that the $TiO_2$ nanoparticles penetrated zebrafish larvae cells; the anatase type (12-14 nm) penetrated the nucleus, and the rutile type (80-100 nm) penetrated the mitochondria. The results of the present study suggest that the toxic effects of $TiO_2$ nanoparticles on zebrafish embryogenesis depend on the crystalline phase and size of the nanoparticles.