The damage, most of which occurred in Hendry and Collier, two of the state's largest citrus producing counties, is likely to have knock-on effects on the price of ingredients and commodities such as orange juice.
Preliminary reports indicate that much of the fruit, which is in the final process of maturing, has been blown off trees, and some trees have been uprooted or are leaning as a result of the severe winds.
"It is difficult for us to adequately gauge the crop loss at this time due to downed communications lines in that area. We hope to have a better assessment by the end of the week," said Florida Citrus Mutual chief executive officer Andy LaVigne.
In addition to crop and tree damage, the growers are concerned that the hurricane could have increased the spread of citrus canker, a bacterial disease that is spread by wind-driven rain.
Citrus canker, which was first detected in Miami in October 1995, was in the process of being eradicated when last year's hurricanes spread the disease across the region. According to LaVigne, the disease has claimed 65,000 acres of grove acreage this year alone.
Before Hurricane Wilma hit this week, Florida's citrus industry had gradually started to get back into shape after last year's disease and natural disaster.
Earlier this month, the US Department of Agriculture (USDA) had announced that it expected the state to turn out 27 percent more oranges this year, forecasting the production of 190 million boxes of oranges, 24 million boxes of grapefruit and 8.3 million boxes of specialty fruit.
These figures, which were still well below the pre-hurricane levels before 2004, are likely to fall even further, with inevitable effects on prices for the fruit juices and ingredients derived from these.
"Growers get more money for their fruit in the fresh market, so this will now be their number one priority. Commodities such as fruit juice and ingredients will take second place," said Mike Yeder, international marketing director at the Florida Department of Citrus (FDOC).
Indeed, the industry's long-term outlook remains uncertain. Southeastern Florida, famous for its high-quality grapefruit and oranges, is also one of the fastest-growing areas for both commercial and residential development.
Some growers feel that the threat of canker, more hurricanes and - most recently - citrus greening disease, a plant condition from China that has been found in southeast Florida and appears to be spreading, make it too risky to replant.
Yet as the industry struggles, demand for the fruit is on the rise. Increased citrus consumption fits with the general trend towards growing consumer awareness about nutrition and health.
"Our research shows that consumers are becoming more aware of the nutritional quality of their foods and how that affects their health and well-being," Dan Gunter, director of FDOC had said earlier this month. "This is the foundation for our marketing programs, and we are very optimistic that consumer demand for naturally nutritious foods, such as 100 percent orange juice and grapefruit juice will increase.
"Orange juice and grapefruit juice are some of the most naturally nutrient-rich beverages on the market. Our job at FDOC is to make sure that story is heard and understood by consumers."
The Florida citrus industry has a $9.1 billion economic impact to the state, employs nearly 90,000 people and covers 750,000 acres in the state.