The etiology of xyloporosis, a disease that has severe effects on citrus trees grafted onto certain citrus rootstocks, was enigmatic for a long time. Symptoms on test hosts following transmission through grafting suggested that it was synonymous with citrus cachexia, a disease that mainly affects mandarin trees. Recent molecular studies have confirmed that certain Hop stunt viroid (HSVd) isolates induce cachexia and xyloporosis symptoms in disease-sensitive citrus hosts. These HSVd infections are mostly symptomless in numerous Near East and Western Mediterranean fruit trees and grapevines; including plants widely cultivated in those regions for several millennia, long before the emergence of xyloporosis and cachexia as diseases of citrus trees. The present review tracks historical changes in citrus propagation practices and the pathological consequences of those changes that contributed to the emergence of xyloporosis as an economically significant disease of citrus trees grafted onto Palestinian sweet lime rootstocks. The take-home message of these accounts is the need for close cooperation between plant scientists, plant protection scientists, and growers to ensure that changes and proposed improvements in horticultural and plant protection practices are subjected to comprehensive risk-assessment analyses.