Extremophilic fungi have surprising powers, surviving and growing under inhospitable conditions including high salinity and high temperatures. These abilities make them formidable enemies in food and agricultural environments. Considering these fungi as a continuum in both environments offers a novel way to examine problems that can arise in the field and end on the shelf. Challenging long-held notions about where spoilage fungi can originate, sea salts were examined as potential sources of low water activity spoilage fungi and were found to contain spoilage-species of Aspergillus, Penicillium, and Cladosporium. Exploring another group of extreme fungi, the farm-to-food transmission route of the heat-resistant spoilage mold, Paecilomyces niveus (Byssochlamys nivea) was elucidated. It was found in a third of New York orchard soils sampled. Experimental inoculations demonstrated its ability to cause a postharvest disease of apples in accordance with Koch’s postulates. The disease was later demonstrated on developing fruit in apple orchards. The newly described disease, Paecilomyces rot, caused by P. niveus presents with symptoms including circular, concentrically-ringed, brown lesions. Its firm, U-shaped internal rot resembles other fungal apple diseases. Importantly, Paecilomyces niveus was observed to produce its heat-resistant ascospores inside apples. When infected apples were used to make juice concentrate using common industry protocols, with stringent thermal processing, some ascospores survived in the finished product. The results suggest that when lesser-quality apples, infected with P. niveus, are used to make concentrate they may introduce spoilage inoculum as well as patulin, the most significant apple mycotoxin. To evaluate control methods for this new disease in the field, the efficacy of EC50 concentrations of difenoconazole, fludioxonil, and pyrimethanil, three active ingredients in fungicides, were tested on thirty P. niveus isolates. Cultures from agricultural environments, likely to have been previously exposed to fungicides, were found to be less sensitive than cultures from environments, such as food, where prior exposure was unlikely. Although resistance does not appear to be widespread, the exposed isolates were significantly less sensitive to fludioxonil. Future research should explore the spoilage implications of this apple disease, its incidence and etiology, and its control before and after harvest.