To set the marker color, use the property markerfacecolor, but for the border color - markeredgecolor:
import matplotlib.pyplot as plt
import numpy as np
spread = np.random.rand(50) * 100
center = np.ones(25) * 50
flier_high = np.random.rand(10) * 100 + 100
flier_low = np.random.rand(10) * -100
data = np.concatenate((spread, center, flier_high, flier_low), 0)
flierprops = dict(marker='o', markerfacecolor='r', markersize=12,
linestyle='none', markeredgecolor='g')
plt.boxplot(data, flierprops=flierprops)
plt.show()

According to @Spiros, the flierprops dictionary is documented here, like the other boxplot properties: http://matplotlib.org/users/dflt_style_changes.html?highlight=flierprops#boxplot
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