Saudi Arabia’s beekeeping sector comprises traditional and modern frame-hive systems operating under diverse environmental and management conditions. This cross-sectional study characterized 98 purposively selected apiaries participating in the Sustainable Rural Agricultural Development (SRAD) Programme, jointly implemented by the Saudi Ministry of Environment, Water and Agriculture and the Food and Agriculture Organization of the United Nations, across Makkah (n = 42), Jazan (n = 34), Asir (n = 16), Al-Baha (n = 4), and Al-Madinah (n = 2). Data included hive structure, honey production, Varroa occurrence, and beekeeper-reported constraints. Given the purposive and regionally unbalanced sampling, inference was restricted to the surveyed apiaries. Among 54 apiaries maintaining both hive systems, median annual yield was higher in modern than traditional hives (2.67 vs. 1.10 kg/colony; paired Wilcoxon p < 0.001). Yield also differed among regions (Kruskal–Wallis H = 19.07, p < 0.001). In the adjusted model, the proportion of modern hives was positively associated with productivity (β = 0.019; p = 0.001), whereas Varroa percentage was not (p = 0.2644). PCA explained 68.1% of variation in the first two components and supported three exploratory apiary clusters. Among 62 apiaries reporting constraints, imports/biosecurity (25.8%), predators (22.6%), and marketing/value-chain issues (19.4%) predominated. The findings demonstrate substantial heterogeneity among surveyed apiaries and support targeted extension and biosecurity interventions, while representative longitudinal studies and standardized disease diagnostics are needed for national-level inference.

Significant regional variation was observed in colony composition, productivity, and disease prevalence. Modern colonies (colonies housed in frame hives) produced significantly higher honey yields than traditional colonies (horizontal cylindrical wooden hive), and colony composition was a stronger determinant of productivity than disease prevalence. Multiple regression indicated that the proportion of modern colonies positively influenced honey yield, while geographical region was the primary predictor of high Varroa destructor infestation. No significant predictors were identified for high Nosema sp. incidence. PCA and cluster analyses identified four distinct production system typologies differing in colony composition, productivity, and disease burden. Beekeepers identified imported bees, biosecurity risks, predator pressure, inadequate disease management, and marketing constraints as the major challenges affecting sector performance. The findings provide an evidence-based framework for developing a National Honeybee Sector Development Strategy focused on strengthening disease surveillance, biosecurity, extension, advisory and value chain interventions along with conservation and genetic improvement of Apis mellifera jemenitica. These interventions will enhance honey production, reduce colony losses, improve pollination services, and support the long-term sustainability and resilience of Saudi Arabia's apiculture sector.