Deserts are the most frequent locations of terrestrial crude oil contaminations. Nevertheless, the long-term effects of petroleum hydrocarbons on desert ecosystems are still unknown, which makes risk assessment and decision making concerning remediation difficult. This study examined the long-term effects of petroleum hydrocarbons on perennial desert vegetation. The study site was a hyper-arid area in the south of Israel, which was contaminated by a crude oil spill in 1975. The contaminated area was compared to uncontaminated reference areas. The composition of perennial plants 40 yr after the oil spill was not significantly affected by the contamination. However, the size distribution of the two most dominant shrub species, Baker and (Moq.) Iljin., and the only tree species, Savi and (Forssk.) Hayne, were different from the reference. These differences can be explained by decreased recruitment. The estimated recruitment of in the last 40 yr post oil spill was 74% less than recruitment in the reference area. Low recruitment of may in the future lead to the loss of tree cover, which would change the entire ecosystem, as are keystone species on which a number of microorganisms, plants, and animals rely. Remediation of oil spills and preventative measures are recommended.