In Botswana, there is limited data available on the health and nutritional status of the San People (also known as the Basarwa or Bushmen), an Indigenous minority group primarily living in the Ghanzi District. Our aim in this study was to assess anemia prevalence among and anthropometric indices of women and young children in Ghanzi District through a cross-sectional survey. We recruited 367 mother–child pairs (women 15–49 years and children 6–59 months) in nine randomly selected areas. A capillary blood sample was collected, and weight and height were measured. Hemoglobin (Hb) concentration was measured with use of a hemoglobinometer (HemoCue, AB), as per global recommendations. Overall, adjusted anemia prevalence was 12% in non-pregnant women (Hb < 120 g/L), 26% in pregnant women (Hb < 110 g/L), and 42% in children (Hb < 110 g/L), but it varied widely depending on whether or not the controversial factor of ethnicity was adjusted for (range of 6–26%, 22–30%, and 35–68% prevalence, respectively). Thirty-nine percent (n = 133/344) of non-pregnant women and 52% (n = 12/23) of pregnant women were underweight (BMI < 18.5 kg/m2). In children aged 6–23 months, 41% were underweight (weight-for-age z-score < −2 SD), 13% were wasted (weight-for-height z-score < −2 SD), and 65% were stunted (height-for-age z-score < −2 SD); in children aged 24–59 months, 57% were underweight, 13% were wasted, and 66% were stunted. Fifty-six percent (n = 205/367) of women self-reported smoking in any form (rolled cigarettes or snuffing). The high prevalence of smoking among women, underweight status among pregnant women, and anemia, stunting, and wasting among children is of the highest concern for public health and should be addressed in future health and nutrition programming.