Protein aggregation is a biochemical hallmark of fatal neurodegenerative disease. Protein disaggregation represents an innovative and appealing therapeutic strategy for the treatment of these protein-misfolding disorders in that it simultaneously reverses: (a) loss-of-function phenotypes associated with sequestration of functional soluble protein into misfolded oligomers and insoluble aggregates; and (b) any toxic gain-of-function phenotypes associated with the misfolded conformers themselves. In Saccharomyces cerevisiae, the AAA+ protein disaggregase Hsp104 increases fitness under stress by reversing stress-induced protein aggregation. Hsp104 is conserved among all nonmetazoan eukaryotes and eubacteria, but is curiously absent in metazoa. Hsp104 activity against protein aggregates associated with neurodegenerative disease is limited. We have engineered Hsp104 variants to antagonize proteotoxic misfolding linked to human neurodegenerative diseases. These engineered Hsp104 variants potently eradicate misfolded structures but can exhibit off-target toxicity, which may limit their therapeutic utility. Here, we assess the possibility that natural Hsp104 homologs might exist with enhanced, selective activity against neurodegenerative disease substrates. First, we report two structures of Hsp104 from the thermophilic fungus Calcarisporiella thermophila (CtHsp104): a 2.70 Å crystal structure and a 4.0 Å cryoelectron microscopy structure. Both structures reveal left-handed, helical assemblies with all domains clearly resolved. We thus provide the highest resolution and most complete view of Hsp104 hexamers to date. We also establish that CtHsp104 antagonizes several toxic protein-misfolding events in vivo where S. cerevisiae Hsp104 is ineffective, including rescue of TDP-43, polyglutamine, and alpha-synuclein (aSyn) toxicity. Next, we hypothesized that therapeutic Hsp104s may be pervasive across extant Hsp104 sequence space. To assess this possibility, we screened a cross-kingdom collection of Hsp104 homologs in several yeast proteotoxicity models. We uncovered therapeutic genetic variation among several Hsp104 homologs that specifically antagonize TDP-43 or aSyn condensate formation and toxicity in yeast, human cells, and C. elegans. Surprisingly, this variation manifested as increased passive chaperone activity, distinct from disaggregase activity, which neutralizes proteotoxicity of specific substrates. Thus, by exploring natural Hsp104 sequence space, we elucidated enhanced, substrate-specific agents to counter proteotoxicity underlying neurodegenerative diseases. Our findings suggest that rational tuning of Hsp104 passive chaperone activity may enable development of substrate- selective disaggregases.