In the great Zoological Gardens we found specimens of all the animals the world produces, I think, including a dromedary, a monkey ornamented with tufts of brilliant blue and carmine hair—a very gorgeous monkey he was—a hippopotamus from the Nile, and a sort of tall, long-legged bird with a beak like a powder horn and close-fitting wings like the tails of a dress coat. This fellow stood up with his eyes shut and his shoulders stooped forward a little, and looked as if he had his hands under his coat tails. Such tranquil stupidity, such supernatural gravity, such self-righteousness, and such ineffable self-complacency as were in the countenance and attitude of that gray-bodied, dark-winged, bald-headed, and preposterously uncomely bird! He was so ungainly, so pimply about the head, so scaly about the legs, yet so serene, so unspeakably satisfied! He was the most comical-looking creature that can be imagined.
It was good to hear Dan and the doctor laugh—such natural and such enjoyable laughter had not been heard among our excursionists since our ship sailed away from America. This bird was a godsend to us, and I should be an ingrate if I forgot to make honorable mention of him in these pages. Ours was a pleasure excursion; therefore we stayed with that bird an hour and made the most of him. We stirred him up occasionally, but he only unclosed an eye and slowly closed it again, abating no jot of his stately piety of demeanor or his tremendous seriousness. He only seemed to say, “Defile not Heaven’s anointed with unsanctified hands.” We did not know his name, and so we called him “The Pilgrim.” Dan said:
“All he wants now is a Plymouth Collection.”
The boon companion of the colossal elephant was a common cat! This cat had a fashion of climbing up the elephant’s hind legs and roosting on his back. She would sit up there, with her paws curved under her breast, and sleep in the sun half the afternoon. It used to annoy the elephant at first, and he would reach up and take her down, but she would go aft and climb up again. She persisted until she finally conquered the elephant’s prejudices, and now they are inseparable friends. The cat plays about her comrade’s forefeet or his trunk often, until dogs approach, and then she goes aloft out of danger. The elephant has annihilated several dogs lately that pressed his companion too closely.
(Innocents Abroad)

Robert Regan, in The Reprobate Elect in The Innocents Abroad offers that the entire episode in the Zoological Gardens of Marseilles is a fiction.  

"On the morning of 12 July they completed the twenty-hour return trip to Marseilles. They checked back into the same hotel. There Mark Twain must have written his Alta letter dated "Paris, July 12th, I867," and there Jackson probably finished his long letter to the Democrat dated "Paris, July 11, I867." Would these two, having just returned from Paris, where they packed ten days' sightseeing into five-including, Mark Twain says, the Jardin des Plantes with its famous ménagerie (IA, Ch. 15, p. 150)-heavy with fatigue from a day and night in the cramped French cars and faced with journalistic deadlines of sorts, have scurried off with Dan, a man with tastes quite as worldly as their own, to Marseilles' dinky little zoo? And would they have spent an hour there, stirring up an old stork, "pimply about the head . . . scaly about the legs," simply to discharge some of their animosity against the pilgrims? Unlikely on all scores, and most of all because these three men had apparently not at that point developed any special animosity toward the people Mark Twain would after the fact style pilgrims. "The Pilgrim" bird seems, then, to come from a fabulous bestiary. This intrusion of fiction into a work of almost journalistic reliability should assure us that the author knew what he was about-that he perceived the need for early treatment of the pilgrims as the boys' antagonists and as their foils."

From a correspondence with Robert Hirst of The Mark Twain Project via Twain-L  (April 4, 2022), it seems there is some dispute regarding Mark Twain's visit to the zoo.  

"But the Jardin Zoologique was hardly “remote”: it was less than a mile away from their hotel, an easy carriage ride, and visiting it might have preceded (or followed) their other “objects of interest,” even though Jackson does not mention it. Other passengers easily made the trip. On 5 July Emily Severance recorded that, along with her husband Solon and Mary Mason Fairbanks, she visited the Zoological Gardens, describing them as having “extensive grounds beautifully laid out. . . . The trees are large, the gardens fine, undulating, rock work with water playing over it, cages of singing birds of all kinds, wild and domestic land and aquatic, animals of every sort.” Passenger William James visited it as well, noting that he had seen ostriches, monkeys, a baboon, an elephant, as well as a “white stork with pink legs.” Mark Twain’s ingenious embroidery of that stork does not make the passage into that rarity in *Innocents*, a pure fiction."