Answer: You didn't give a detailed description of the spots, so I don't know if it is a cultural, environmental or disease problem. There are several peach tree diseases that can cause brown spots on fruits (among other symptoms). The most common are:
Brown Rot - Brown rot attacks flowers, shoots and fruit. Diseased flowers wilt and turn brown very quickly. Shoot infections result in fairly small elongated (1-3 inches long) gummy cankers. These cankers will provide the disease spores for fruit rot.
Brown rot is the most common fruit rot. A tan to brown spot appears on the surface of diseased fruit. In humid weather, brownish tufts of spores appear on the rotted surface. Infected fruit will rot completely to become a mummy. The mummies carry the disease over the winter. Sanitation is a valuable part of brown rot control in the home orchard. Collecting diseased fruit as soon as it appears and removing infected twigs and mummies from the trees will reduce the carry-over of brown rot to the next season. If fruit ripening occurs during a period of warm, wet weather, a very rigid spray program is required to control brown rot. It is important to begin spraying just before the fruit ripens. Delaying a spray program until rotten fruit is evident will result in very poor control regardless of the effort.
Peach Scab - This disease appears as small (usually less than 1/8 inch in diameter) dark, somewhat velvety spots on fruit. Large black areas may result from numerous closely spaced infections. This disease is easily controlled with chemical sprays applied at the "shuck split" stage and every 14 days for the next four to six weeks. Shuck split is the stage after bloom when the dry flower parts split and fall free of the small green fruit. Disease symptoms occur only on the outer skin. Infected fruit looks bad but eating quality is not affected. Peel fruit to remove all traces of the disease.
Rhizopus Rot - This disease occurs on ripe or nearly ripe fruit. Infected peaches turn brown. The rotted areas are very soft and will become covered with coarse black fungal growth. This disease is very common on peaches harvested and stored at room temperature a few days before consumption. Chemical sprays just before harvest and careful handling at harvest will help control rhizopus rot.
Bacterial Spot - Bacterial spot is a disease of peach fruit and leaves. Infected leaves develop small reddish-purple spots, often with white centers. These spots often drop out giving the leaf a tattered or "shot hole" appearance. Infected leaves turn yellow and drop. This leaf loss weakens the tree. Infections on fruit appear as small dark spots. Close examination reveals these spots to resemble open sores rather than the velvety spots characteristic of peach scab. In years of severe infection, diseased areas of the fruit may develop severe cracks.
Hope the above descriptions will help you determine the cause of the brown spots.
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