In 1909, the first specimen of Paecilomyces niveus Stolk & Samson (Byssochlamys nivea Westling) was isolated from a specimen of Geaster that was stored in alcohol, a prelude to the remarkably persistent properties of this fungus food makers would later come to grips with. In the century since, this heat resistant mold P. niveus has continued to spoil normally shelf-stable fruit products. This is particularly alarming contamination because the fungus produces patulin, a known and regulated mycotoxin. It has been long assumed that P. niveus spoilage inoculum originates from environmental sources like air, soil, and infested equipment, but recently, the fungus was found to cause the postharvest apple disease Paecilomyces rot, capable of infecting and growing in live apple fruits. Processing infected apples can result in highly infested and mycotoxin-contaminated cider, a finding that fundamentally changes how we view sources of P. niveus spoilage inoculum. In the first chapter of this dissertation, I review previous work and new developments regarding research on P. niveus, focusing on 1). The economic impact and extremotolerant properties of this fungus and 2). How the new understanding that P. niveus causes plant disease can drive future research in this field. In chapters two and three, I investigate the host range of Paecilomyces rot and the infection biology of P. niveus. I determined that various rosaceous and citrus fruits are susceptible to infection by P. niveus, and established cultivar-based susceptibility in apple fruits. In chapter 4, I developed species-specific primers based on the patK gene, encoding a 6-methylsalicylic acid synthase, and validated a new qPCR system designed to detect P. niveus in food, fruit, and soil. The qPCR system was used to investigate questions regarding P. niveus disease biology using apple blossom and strawberry bioassays. Lastly, in chapter 5 I assess risk of spoilage and contamination in hard apple cider by four patulin-producing apple pathogens. Our results support my hypothesis that bench-top fermentation does not sufficiently preclude P. niveus spoilage and patulin contamination in finished product. Results from these studies will aid food producers in better understanding and assessing risk factors of P. niveus spoilage and patulin contamination in fruit products.