We screened 85 isolates of Bacillus thuringiensis (Berliner), making up 57 different subspecies, and two isolates of Bacillus sphaericus (Meyer and Neide) for activity against immature horn flies, Haematobia irritons (L.), and stable flies, Stomoxys calcitrans (L.). The majority of B. thuringiensis and the B. sphaericus isolates had little or no activity against horn fly and stable fly. Approximately 87% of the isolates caused <50% mortality of horn fly larvae and 64% caused <25% mortality. For stable fly, 95% of the isolates caused <50% mortality, and 93% caused <25% mortality. Five isolates were highly toxic to horn fly and stable fly immatures. These isolates were B. t. tolworthi 4L3, B. t. darmstadiensis 4M1, B. t. thompsoni 4O1, B. t. thuringiensis HD2, and B. t. kurstaki HD945. The LD₅₀ values ranged from 2.2 to 7.9 × 10⁶ spores per g manure for horn fly and from 6.3 to 35 × 106 spores per g media for stable fly. These were consistently more toxic compared with the B. t. israelensis isolates examined. All had DNA that hybridized with cry1Aa, cry1Ab, and cry1Ac toxin probes, three hybridized with a cry1B probe, and two hybridized with a cry2A probe. These may have potential for use in integrated management of pest flies.