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<i>Anaplasma phagocytophilum</i> (<i>A. phagocytophilum</i>) is the aetiological agent of tick-borne fever in cattle and sheep, and granulocytic anaplasmosis in human and dogs. Livestock, companion animal and human infections with <i>A. phagocytophilum</i> have been reported globally. Across England and Wales, two isolates (called ecotypes) have been reported in ticks. This study examined <i>A. phagocytophilum</i> isolates present in livestock and wildlife in Great Britain (GB), with a particular focus on cattle. Clinical submissions (EDTA blood) from cattle (<i>n</i> = 21) and sheep (<i>n</i> = 3) were received by APHA for tick-borne disease testing and the animals were confirmed to be infected with <i>A. phagocytophilum</i> using a PCR targeting the <i>Msp</i>2 gene. Further submissions from roe deer (<i>n</i> = 2), red deer (<i>n</i> = 2) and <i>Ixodes ricinus</i> ticks (<i>n</i> = 22) were also shown to be infected with <i>A. phagocytophilum</i>. Subsequent analysis using a nested PCR targeting the <i>groEL</i> gene and sequencing confirmed the presence of ecotype I in cattle, sheep, red deer and <i>Ixodes ricinus</i>, and ecotype II in roe deer and <i>I. ricinus</i> removed from deer carcasses. Despite the presence of two ecotypes, widely distributed in ticks from England and Wales, only ecotype I was detected in cattle in this study.