Agriculture is currently progressing towards sustainable pest management systems in which synthetic organic pesticides are no longer essential in the fight against pests, with a tendency to reduce their usage, as in integrated pest management, or to eliminate them entirely, as in organic farming. Emphasis is placed in methodologies related to the knowledge of the physiology of insects, such as mating disruption, or the understanding and management of the agro-ecosystem, including biological control. Europe is currently advocating for different pest management regulations that would prioritize non pollutant management methods and the protection of biodiversity. However, few studies have evaluated the effects of different pest management systems on auxiliary fauna and biodiversity in Mediterranean tree crops. We conducted a study based on periodical samples taken between 2006 and 2008 on 41 commercial orchards in the district of La Ribera Alta (Valencia), in order to evaluate the effect of pest management system on arthropod abundance and diversity of beneficial species. Of all the plots, 14 were persimmon, of which 9 were conventional and 5 organic farming; 15 were citrus (9 conventional and 6 organic) and 12 were nectarine (9 conventional and 3 organic). Samples were collected with an engine-powered vacuum-machine, yellow sticky traps and Berlese funnel. The arthropod orders that were generally most abundant in crops and cropping systems were Hymenoptera, Diptera and Hemiptera. The phytophagous families found to be more abundant in organic farming were thripidae in the three crops, while in conventional farming, thripids were the most abundant in nectarine; tephritids the most numerous in persimmon; and aphids in citrus. Among the Chalcidoidea, the most abundant families were encirtids, aphelinids, mimarids, eulophids, pteromalids and trichogramatids. The most abundant species were Metaphycus flavus, Aphytis melinus, Stethynium triclavatum, Cales noacki, Syrphophagus aphidivorus, Anagrus atomus, Alaptus spp., Ceranisus lepidotus and Metaphycus helvolus. As regards the predators, we studied the ladybird family, the most abundant species being Stethorus punctillum, Scymnus spp. Rodolia cardinalis and Propylea quatuordecimpunctata. When analyzing all species together, the organic farming system significantly increased the abundance of auxiliary insects by nearly 50%, while richness and biodiversity by approximately 25%, compared to the conventional farming system. This increase is variable depending on the crop, higher in persimmon and nectarine than in citrus, and on the other hand, depending on the functional group of the auxiliary insect, for example, higher in predators than in parasitoids. When considering the different families separately, abundance increased significantly in the case of coccinellids and mimarids, whereas biodiversity increased significantly only in cocinellids. We found a significant relationship between the abundance of natural enemies and herbivores: is the case of the coccinellid Stethorus punctillum with tetranychid mite Tetranychus urticae; mimarids Stethynium triclavatum and Anagrus atomus with leafhoppers; and eulophid Ceranisus with thrips. A good correlation was found between the indices based on richness and evenness obtained at the species level and those obtained at the family level, indicating that the use of the family taxon for biodiversity studies could be a valid alternative for simplifying future studies of a similar nature. Some species of natural enemies are much more abundant in organic farming plots, regardless of crop type, and would thus be good candidates to be used as indicators of quality or environmental sustainability. These species are Scymnus spp., Encarsia perniciosi, Stethynium triclavatum and Anagrus atomus.