Two-dimensional (2D) boron (that is, borophene) was recently synthesized following theoretical predictions1-5. Its metallic nature and high in-plane anisotropy combine many of the desirable attributes of graphene6 and monolayer black phosphorus7. As a synthetic 2D material, its structural properties cannot be deduced from bulk boron, which implies that the intrinsic defects of borophene remain unexplored. Here we investigate borophene line defects at the atomic scale with ultrahigh vacuum (UHV) scanning tunnelling microscopy/spectroscopy (STM/STS) and density functional theory (DFT). Under suitable growth conditions, borophene phases that correspond to the v1/6 and v1/5 models are found to intermix and accommodate line defects in each other with structures that match the constituent units of the other phase. These line defects energetically favour spatially periodic self-assembly that gives rise to new borophene phases, which ultimately blurs the distinction between borophene crystals and defects. This phenomenon is unique to borophene as a result of its high in-plane anisotropy and energetically and structurally similar polymorphs. Low-temperature measurements further reveal subtle electronic features that are consistent with a charge density wave (CDW), which are modulated by line defects. This atomic-level understanding is likely to inform ongoing efforts to devise and realize applications based on borophene.