Diagnosis. It belongs to the annulicornis species-group, and can be separated from other species within that group based on the combination of T2 mostly smooth and polished, antenna brown with flagellomeres 6–8 white (rarely also posterior half of flagellomere 5, white band clearly occupying less than one third of antenna length), and metasoma with T3+ partially brown. Those features are shared with the morphologically similar P. luisguillermosolisi, but P. margaritapenonae has darker areas on propodeum, metapleuron, metascutellum and axillar complex, while luisguillermosolisi has the mesosoma entirely orange-yellow.
Description. Female. Body length 2.2–2.3 mm or 2.4–2.5 mm. Fore wing length 2.4–2.5 mm or 2.6–2.7 mm. Head color: mostly dark brown to black; except for orange on most of frons and face, and yellow clypeus, labrum, mandibles, and spot on lower corner of gena near oral foramen. Flagellomere color: central flagellomere white-yellow, rest dark brown to black. Mesosoma color: orange to yellow-orange, with propodeum, metascutellum and parts of axillar complex darker than rest of mesosoma; rarely anteromesoscutum with dark marks laterally and centrally on anterior 0.3. Metasoma color (dorsally): mediotergites 1–2 orange-yellow, rest of mediotergites brown. Coxae color: all pale. Metatibia color: pale. Metatarsus color: pale. Pterostigma color: entirely dark, rarely mostly dark, but with anterior pale spot. Mediotergite 1 length/width at posterior margin 4.1–4.5 × or 4.6–5.0 ×. Mediotergite 1 maximum width/width at posterior margin 2.3–2.4 × or 2.5–2.6 ×. Mediotergite 2 width at posterior margin/length: 2.9–3.1 x, 3.2–3.3 x, rarely 3.4–3.5 ×. Mediotergite 2 sculpture: Mostly smoth and polished. Ovipositor sheaths length: 0.7 × as long as metatibia. Male. As female, but with all flagellomeres brown and darker body coloration (especially on anteromesoscutum and propodeum).
Pseudapanteles margaritapenonae is rather variable morphologically, with color varying from very dark brown (including marks on anteromesoscutum) to almost lacking dark areas. The latter extreme approaches the coloration of P. luisguillermosolisi. However, these species differ as described in the diagnosis and the comments for P. luisguillermosolisi.