This dataset investigated the diversity, the geographic and spatial distribution of haematophagous flies collected from cattle farms in Peninsular Malaysia. Biting flies were trapped from 25 cattle farms over a one-year period. One-way Analysis of Variance (ANOVA) was used to establish the presence/absence of statistical differences in the number of flies caught in relation to the different geographic distributions (zones). Three thousand eight hundred and eighty-nine haematophagous flies comprising of 36 different species, including species (3189; 82.0%), species (588; 15.1%), species (58; 1.5%), species (19; 0.5%), (3; 0.1%), species (29; 0.7%) and (3; 0.1%) were collected using three different types of fly traps. More biting flies were trapped in the southwest (1070; 27.5%) and south (1045; 26.9%) zones compared to other arbitrary zones of Peninsular Malaysia. Haematophagous flies were spatially distributed both in the inland and coastal parts of the country. The difference in the catch of species within zones was not significant (F = 1.299; df = 5;  = 0.306), although it was highest in the southwest zone. The number of species caught was highest in the south zone compared to other zones, the differences was not significant (F = 0.770; df = 5;  = 0.583). Tabanidae fly species were most abundant in the southwest zone, the differences among zones was not significant (F = 1.179; df = 5;  = 0.356).