The I-Mn-V antiferromagnet, NaMnBi, develops a very large positive magnetoresistance (MR) up to 10,000% at 2 K and 9 T in crystals showing a semiconductor-to-metal transition (SMT). In the absence of an SMT, a modest (20%) MR is achieved. Here, we show that upon cooling below the magnetic transition, a spatial modulation appears giving rise to new Bragg peaks due to charge and defect ordering in a checkerboard pattern, with two kinds of modulation vectors, $q_1$=($frac23$, 0, 1) and $q_2$=($frac23, frac13, frac12$). This constitutes a superlattice transition ($T_s$) that lowers the symmetry from the high temperature centrosymmetric P4/nmm to the non-centrosymmetric P$overline4$m2. In crystals with a large MR, a close to room temperature $T_s$ is observed with $q_1$ appearing first, followed by $q_2$. In crystals with low MR however, $T_s$ is much lower and only $q_1$ is observed. The charge modulation and spin fluctuations may both contribute to the enhancement of MR.
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