A series of experiments was conducted with apple (Malus ×domestica) and peach [Prunus persica (L.) Batsch] from 2003 to 2008 to evaluate the flower thinning efficacy of eugenol and a eugenol-based essential oil. Flower thinning effects by hand defoliation and alternative chemical agents were compared with eugenol in different years. Eugenol or the eugenol-based contact herbicide Matran 2 EC (or Matratec AG) produced noticeable phytotoxicity to floral parts and exposed leaf tissue within 15 min to 1 h after application and injury was proportional to rate. At the highest rates (8% and 10%), eugenol resulted in complete burning of all exposed tissue except bark tissue, in which there were no visible signs of injury. Within 3 to 4 weeks of application, phytotoxicity was difficult to observe even at the higher rates of eugenol. In companion experiments, hand defoliation of young leaves at bloom resulted in abscission of young fruitlets in apple, but not in peach, indicating that eugenol may cause thinning by multiple mechanisms. Ammonium thiosulfate (ATS) [49 L·ha−1 or 6.0% (v/v)] provided thinning in peach and showed little or no phytotoxicity, but the response was inconsistent. ATS was also inconsistent in thinning apple. The thinning response from monocarbamidedihydrogen sulphate (MCDS; Wilthin) at 3.2% (v/v) was inconsistent in peach. At the rate used, MCDS caused some phytotoxicity on peach. Applications of 1% to 2% eugenol appear promising, but good blossom coverage is critical for thinning. Furthermore, eugenol formulations need improvement to ensure uniform coverage for more predictable thinning.