Anaplasmosis is a tick-borne disease that can result in serious loss of production and even loss of livestock. It is caused by the most globally prevalent vector-borne pathogen of livestock, Anaplasma marginale, with endemic regions in all six permanently inhabited continents. This study examined the occurrence and diversity of A. marginale in cattle (n= 100) opportunistically sampled at two diptanks (Botao, n=50, and Namitangurine, n=50) in Zambezia Province, Mozambique. A duplex quantitative real-time PCR was used to detect A. marginale and A. marginale subsp. centrale in cattle samples from the two diptanks. The overall prevalence of A. marginale was 87% (95% CI: 80, 93%). There was no significant difference (p>0.05) between the prevalence of A. marginale in cattle at Namitangurine diptank (88.0%, n=42) and Botao diptank (86.0%, n=43). The overall prevalence of A. marginale subsp. centrale was 6.0% (95% CI: 2.0, 11%). Only 2.0% (n=1) of cattle sampled from Botao diptank were positive for A. marginale subsp. centrale, while 10% (n=5) were positive for A. marginale subsp. centrale at Namitangurime diptank. There was no significant association (p>0.05) between A. marginale subsp. centrale presence in cattle and diptank. In order to assess the genetic variability in A. marginale, msp1α amplicons were sequenced from 27 samples from the two diptanks. Fourteen novel MSP1a repeat sequences were identified. Most samples had mixed infections with one to eight msp1α genotypes identified in individual animals. A total of 47 different msp1α genotypes were found from 76 msp1α sequences generated from the 27 samples. This considerable genetic diversity contributes to the understanding of the regional diversity of A. marginale and will be important for the development of appropriate and effective vaccines in the future. In future research, the gene sequences of eight highly promising vaccine candidates will be examined from these samples. In addition, the results will be compared to equivalent results from cattle samples from an area in the Limpopo National Park where cattle are grazed alongside wildlife, to see if the presence of wildlife affects the diversity of the A. marginale population in cattle.