The availability of large datasets of organism images combined with advances in artificial intelligence (AI) has significantly enhanced the study of organisms through images, unveiling biodiversity patterns and macro-evolutionary trends. However, existing machine learning (ML)-ready organism datasets have several limitations. First, these datasets often focus on species classification only, overlooking tasks involving visual traits of organisms. Second, they lack detailed visual trait annotations, like pixel-level segmentation, that are crucial for in-depth biological studies. Third, these datasets predominantly feature organisms in their natural habitats, posing challenges for aquatic species like fish, where underwater images often suffer from poor visual clarity, obscuring critical biological traits. This gap hampers the study of aquatic biodiversity patterns which is necessary for the assessment of climate change impacts, and evolutionary research on aquatic species morphology. To address this, we introduce the Fish-Visual Trait Analysis (Fish-Vista) dataset—a large, annotated collection of about 80K fish images spanning 3000 different species, supporting several challenging and biologically relevant tasks including species classification, trait identification, and trait segmentation. These images have been curated through a sophisticated data processing pipeline applied to a cumulative set of images obtained from various museum collections. Fish-Vista ensures that visual traits of images are clearly visible, and provides fine-grained labels of various visual traits present in each image. It also offers pixel-level annotations of 9 different traits for about 7000 fish images, facilitating additional trait segmentation and localization tasks. The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI. Finally, we provide a comprehensive analysis of state-of-the-art deep learning techniques on Fish-Vista.