The accumulation of tau, a soluble and microtubule-associated protein, into insoluble intraneuronal aggregates known as neurofibrillary tangles (NFTs) is a pathological hallmark of Alzheimer’s disease (AD), a devastating neurological disorder. Given the strong correlation between the presence of NFTs at specific brain regions and the severity of AD clinical symptoms and neuropathological features, tau aggregation is considered to be a key pathological event in AD. Emerging evidence suggests that small, soluble tau oligomers rather than NFTs constitute toxic entities in AD. However, visualizing and characterizing these species within intact cellular models and human brain tissues pose a challenge, as traditional light microscopy techniques are incapable of resolving biologic complexes smaller than 250 nm. Here, we utilize super-resolution microscopy to visualize and characterize both physiological and pathological nanoscale tau oligomers within engineered cellular models as well as in postmortem human brain tissue from individuals exhibiting Primary Age-Related Tauopathy (PART), intermediate and advanced AD and tau-pathology-free controls. Our results show that tau nano-aggregates phosphorylated at residues T231 and T181 are present in control cases, whereas p-S202/T205 positive nano-aggregates are specifically associated with AD and, to a lesser extent, observed in PART. This finding suggests distinct phosphorylation signatures distinguishing physiological from pathological tau nano-aggregates. Moreover, nano-aggregates exhibit morphological differences between AD and non-AD conditions, increasing in size and complexity in AD. In advanced AD, tau nano-aggregates contain multiple distinct phosphorylated residues, whereas intermediate AD nano-aggregates are predominantly marked by a single phosphorylated residue. Our findings reveal novel transitions in the morphology and phosphorylation states of tau nano-aggregates as they shift from physiological to pathological forms. The ability to detect and profile physiological and pathological nanoscale tau aggregates in human brain tissues opens new avenues for studying the molecular underpinnings of tauopathies.